Quasi-RAW

Simple example.

Example on how to run the quasiraw pre-processing using BrainPrep. See user guide for details.

Data

Let’s first get some anatomical data: T1w, T2w and FLAIR.

from pathlib import Path
from brainprep.utils import Bunch
from brainprep.datasets import OpenMSDataset

datadir = Path("/tmp/brainprep-data")
datadir.mkdir(parents=True, exist_ok=True)
dataset = OpenMSDataset(datadir)
data = Bunch()
for modality in ("T1w", "T2w", "FLAIR"):
    data[modality] = Bunch(
        sub01=dataset.fetch(
            subject="01",
            modality=modality,
            dtype="cross_sectional",
        ),
        sub02=dataset.fetch(
            subject="02",
            modality=modality,
            dtype="cross_sectional",
        ),
    )
print(data)

Bunch(
  T1w: Bunch(
    sub01: Bunch(
      description: PosixPath('/tmp/brainprep-data/rawdata/dataset_description.json')
      anat: PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_T1w.nii.gz')
    )
    sub02: Bunch(
      description: PosixPath('/tmp/brainprep-data/rawdata/dataset_description.json')
      anat: PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_T1w.nii.gz')
    )
  )
  T2w: Bunch(
    sub01: Bunch(
      description: PosixPath('/tmp/brainprep-data/rawdata/dataset_description.json')
      anat: PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_T2w.nii.gz')
    )
    sub02: Bunch(
      description: PosixPath('/tmp/brainprep-data/rawdata/dataset_description.json')
      anat: PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_T2w.nii.gz')
    )
  )
  FLAIR: Bunch(
    sub01: Bunch(
      description: PosixPath('/tmp/brainprep-data/rawdata/dataset_description.json')
      anat: PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_FLAIR.nii.gz')
    )
    sub02: Bunch(
      description: PosixPath('/tmp/brainprep-data/rawdata/dataset_description.json')
      anat: PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_FLAIR.nii.gz')
    )
  )
)

Analysis

Let’s now perform the preprocessing using BrainPrep. As with many tutorials, we won’t execute the code directly here. However, feel free to set the ‘dryrun’ configuration to False to actually run each step and generate results on disk.

import shutil
from brainprep.workflow import (
    brainprep_quasiraw,
    brainprep_group_quasiraw,
)
from brainprep.config import Config

outdir = Path("/tmp/brainprep-quasiraw")
if outdir.is_dir():
    shutil.rmtree(outdir)
outdir.mkdir(parents=True, exist_ok=True)
with Config(dryrun=True, verbose=True):
    for modality, modality_data in data.items():
        for subject_data in modality_data.values():
            outputs = brainprep_quasiraw(
                anatomical_file=subject_data.anat,
                output_dir=outdir,
                keep_intermediate=True,
            )
        outputs = brainprep_group_quasiraw(
            modality=modality,
            output_dir=outdir,
        )

[warn] - BIDS file name does not contain run key: sub-01_T1w.nii.gz
[title] - Subject Level Quasi-RAW...
________________________________________________________________________________
[call] brainprep.workflow.quasiraw.brainprep_quasiraw(
    anatomical_file=PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/su
b-01_T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01'),
    rigid=False,
    quick=False,
    keep_intermediate=True,
    kwargs={'entities': {'sub': '01', 'modality': 'T1w', 'mod': 'T1w', 'ses':
'01', 'run': '34706'}},
)
[info] - setting template file:
/home/runner/work/brainprep/brainprep/doc/../brainprep/resources/MNI152_T1_1mm_b
rain.nii.gz
[info] - setting workspace directory:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706
[command] - brainprep interface reorient -image-file
/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_T1w.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/01-reorient -entities sub-01_modality-T1w_mod-T1w_ses-01_run-34706 -verbose
True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.reorient(
    image_file=PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_
T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_34706/01-reorient'),
    entities={'sub': '01', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'34706'},
)
[command] - fslreorient2std
/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_T1w.nii.gz
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/01-reorient/sub-01_ses-01_run-34706_mod-T1w_reorient.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/01-reorient/sub-01_ses-01_run-34706_mod-T1w_reorient.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface brainmask -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/01-reorient/sub-01_ses-01_run-34706_mod-T1w_reorient.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/02-brainmask -entities sub-01_modality-T1w_mod-T1w_ses-01_run-34706 -verbose
True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.brainmask(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_34706/01-reorient/sub-01_ses-01_run-34706_mod-T1w_reorie
nt.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_34706/02-brainmask'),
    entities={'sub': '01', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'34706'},
)
[command] - mri_synthstrip -i
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/01-reorient/sub-01_ses-01_run-34706_mod-T1w_reorient.nii.gz -o
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/02-brainmask/sub-01_ses-01_run-34706_mod-T1w_brain.nii.gz -m
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/02-brainmask/sub-01_ses-01_run-34706_mod-T1w_brainmask.nii.gz -f 0 --no-csf
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/02-brainmask/sub-01_ses-01_run-34706_mod-T1w_brain.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/02-brainmask/sub-01_ses-01_run-34706_mod-T1w_brainmask.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface biasfield -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/01-reorient/sub-01_ses-01_run-34706_mod-T1w_reorient.nii.gz -mask-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/02-brainmask/sub-01_ses-01_run-34706_mod-T1w_brainmask.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/03-biasfield -entities sub-01_modality-T1w_mod-T1w_ses-01_run-34706 -quick
False -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.ants.biasfield(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_34706/01-reorient/sub-01_ses-01_run-34706_mod-T1w_reorie
nt.nii.gz'),
    mask_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/s
ub-01/ses-01/workspace_34706/02-brainmask/sub-01_ses-01_run-34706_mod-T1w_brainm
ask.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_34706/03-biasfield'),
    entities={'sub': '01', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'34706'},
    quick=False,
)
[command] - N4BiasFieldCorrection -d 3 -i
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/01-reorient/sub-01_ses-01_run-34706_mod-T1w_reorient.nii.gz -s 1 -b
[1x1x1,3] -c [50x50x50x50,0.001] -t [0.15,0.01,200] -x
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/02-brainmask/sub-01_ses-01_run-34706_mod-T1w_brainmask.nii.gz -o
[/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_3
4706/03-biasfield/sub-01_ses-01_run-34706_mod-T1w_biascorrected.nii.gz,/tmp/brai
nprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34706/03-bi
asfield/sub-01_ses-01_run-34706_mod-T1w_biasfield.nii.gz] -v
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/03-biasfield/sub-01_ses-01_run-34706_mod-T1w_biascorrected.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/03-biasfield/sub-01_ses-01_run-34706_mod-T1w_biasfield.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applymask -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/03-biasfield/sub-01_ses-01_run-34706_mod-T1w_biascorrected.nii.gz -mask-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/02-brainmask/sub-01_ses-01_run-34706_mod-T1w_brainmask.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/03-biasfield -entities sub-01_modality-T1w_mod-T1w_ses-01_run-34706 -verbose
True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.applymask(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_34706/03-biasfield/sub-01_ses-01_run-34706_mod-T1w_biasc
orrected.nii.gz'),
    mask_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/s
ub-01/ses-01/workspace_34706/02-brainmask/sub-01_ses-01_run-34706_mod-T1w_brainm
ask.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_34706/03-biasfield'),
    entities={'sub': '01', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'34706'},
)
[command] - fslmaths
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/03-biasfield/sub-01_ses-01_run-34706_mod-T1w_biascorrected.nii.gz -mas
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/02-brainmask/sub-01_ses-01_run-34706_mod-T1w_brainmask.nii.gz
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/03-biasfield/sub-01_ses-01_run-34706_mod-T1w_applymask.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/03-biasfield/sub-01_ses-01_run-34706_mod-T1w_applymask.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface scale -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/03-biasfield/sub-01_ses-01_run-34706_mod-T1w_applymask.nii.gz -scale 1
-output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/04-scale -entities sub-01_modality-T1w_mod-T1w_ses-01_run-34706
-interpolation spline -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.scale(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_34706/03-biasfield/sub-01_ses-01_run-34706_mod-T1w_apply
mask.nii.gz'),
    scale=1,
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_34706/04-scale'),
    entities={'sub': '01', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'34706'},
    interpolation='spline',
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/03-biasfield/sub-01_ses-01_run-34706_mod-T1w_applymask.nii.gz -ref
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/03-biasfield/sub-01_ses-01_run-34706_mod-T1w_applymask.nii.gz -applyisoxfm 1
-interp spline -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/04-scale/sub-01_ses-01_run-34706_mod-T1w_scale.nii.gz -omat
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/04-scale/sub-01_ses-01_run-34706_mod-T1w_scale.txt -verbose 1
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/04-scale/sub-01_ses-01_run-34706_mod-T1w_scale.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/04-scale/sub-01_ses-01_run-34706_mod-T1w_scale.txt
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface affine -anatomical-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/04-scale/sub-01_ses-01_run-34706_mod-T1w_scale.nii.gz -template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T1_1mm_brain.ni
i.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/05-affine -entities sub-01_modality-T1w_mod-T1w_ses-01_run-34706 -rigid
False -quick False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.affine(
    anatomical_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subj
ects/sub-01/ses-01/workspace_34706/04-scale/sub-01_ses-01_run-34706_mod-T1w_scal
e.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T1_1mm_brain.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_34706/05-affine'),
    entities={'sub': '01', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'34706'},
    rigid=False,
    quick=False,
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/04-scale/sub-01_ses-01_run-34706_mod-T1w_scale.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T1_1mm_brain.ni
i.gz -cost normmi -searchcost normmi -anglerep euler -bins 256 -interp trilinear
-dof 9 -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/05-affine/sub-01_ses-01_run-34706_mod-T1w_affine.nii.gz -omat
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/05-affine/sub-01_ses-01_run-34706_mod-T1w_affine.txt -verbose 1
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/05-affine/sub-01_ses-01_run-34706_mod-T1w_affine.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/05-affine/sub-01_ses-01_run-34706_mod-T1w_affine.txt
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applyaffine -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/03-biasfield/sub-01_ses-01_run-34706_mod-T1w_biascorrected.nii.gz
-template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T1_1mm_brain.ni
i.gz -transform-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/05-affine/sub-01_ses-01_run-34706_mod-T1w_affine.txt -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/06-applyaffine -entities sub-01_modality-T1w_mod-T1w_ses-01_run-34706
-interpolation spline -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.applyaffine(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_34706/03-biasfield/sub-01_ses-01_run-34706_mod-T1w_biasc
orrected.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T1_1mm_brain.nii.gz'),
    transform_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subje
cts/sub-01/ses-01/workspace_34706/05-affine/sub-01_ses-01_run-34706_mod-T1w_affi
ne.txt'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_34706/06-applyaffine'),
    entities={'sub': '01', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'34706'},
    interpolation='spline',
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/03-biasfield/sub-01_ses-01_run-34706_mod-T1w_biascorrected.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T1_1mm_brain.ni
i.gz -init
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/05-affine/sub-01_ses-01_run-34706_mod-T1w_affine.txt -interp spline
-applyxfm -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/06-applyaffine/sub-01_ses-01_run-34706_mod-T1w_applyaffine.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/06-applyaffine/sub-01_ses-01_run-34706_mod-T1w_applyaffine.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applyaffine -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/02-brainmask/sub-01_ses-01_run-34706_mod-T1w_brainmask.nii.gz -template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T1_1mm_brain.ni
i.gz -transform-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/05-affine/sub-01_ses-01_run-34706_mod-T1w_affine.txt -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/07-applyaffine -entities sub-01_modality-T1w_mod-T1w_ses-01_run-34706
-interpolation nearestneighbour -verbose True -dryrun True -no-color False
-skip-run-check False -cat12-file /opt/cat12/standalone/cat_standalone.sh
-spm12-dir /opt/cat12 -matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.applyaffine(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_34706/02-brainmask/sub-01_ses-01_run-34706_mod-T1w_brain
mask.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T1_1mm_brain.nii.gz'),
    transform_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subje
cts/sub-01/ses-01/workspace_34706/05-affine/sub-01_ses-01_run-34706_mod-T1w_affi
ne.txt'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_34706/07-applyaffine'),
    entities={'sub': '01', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'34706'},
    interpolation='nearestneighbour',
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/02-brainmask/sub-01_ses-01_run-34706_mod-T1w_brainmask.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T1_1mm_brain.ni
i.gz -init
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/05-affine/sub-01_ses-01_run-34706_mod-T1w_affine.txt -interp
nearestneighbour -applyxfm -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/07-applyaffine/sub-01_ses-01_run-34706_mod-T1w_applyaffine.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/07-applyaffine/sub-01_ses-01_run-34706_mod-T1w_applyaffine.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface copyfiles -source-files
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34
706/06-applyaffine/sub-01_ses-01_run-34706_mod-T1w_applyaffine.nii.gz,/tmp/brain
prep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34706/07-app
lyaffine/sub-01_ses-01_run-34706_mod-T1w_applyaffine.nii.gz,/tmp/brainprep-quasi
raw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_34706/05-affine/sub-01
_ses-01_run-34706_mod-T1w_affine.txt -destination-files
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/sub-01_ses-0
1_run-34706_T1w.nii.gz,/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub
-01/ses-01/sub-01_ses-01_run-34706_mod-T1w_brainmask.nii.gz,/tmp/brainprep-quasi
raw/derivatives/quasiraw/subjects/sub-01/ses-01/sub-01_ses-01_run-34706_mod-T1w_
affine.txt -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01 -move-files
False -dryrun False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.utils.copyfiles(
    source_files=[PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjec
ts/sub-01/ses-01/workspace_34706/06-applyaffine/sub-01_ses-01_run-34706_mod-T1w_
applyaffine.nii.gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/w
orkspace_34706/07-applyaffine/sub-01_ses-01_run-34706_mod-T1w_applyaffine.nii.gz
'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/w
orkspace_34706/05-affine/sub-01_ses-01_run-34706_mod-T1w_affine.txt')],
    destination_files=[PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/s
ubjects/sub-01/ses-01/sub-01_ses-01_run-34706_T1w.nii.gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/s
ub-01_ses-01_run-34706_mod-T1w_brainmask.nii.gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/s
ub-01_ses-01_run-34706_mod-T1w_affine.txt')],
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01'),
    move_files=False,
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[title] - Subject Level Quasi-RAW done.
__________________________________________________________________0.09s, 0.00min
[warn] - BIDS file name does not contain run key: sub-02_T1w.nii.gz
[title] - Subject Level Quasi-RAW...
________________________________________________________________________________
[call] brainprep.workflow.quasiraw.brainprep_quasiraw(
    anatomical_file=PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/su
b-02_T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01'),
    rigid=False,
    quick=False,
    keep_intermediate=True,
    kwargs={'entities': {'sub': '02', 'modality': 'T1w', 'mod': 'T1w', 'ses':
'01', 'run': '21669'}},
)
[info] - setting template file:
/home/runner/work/brainprep/brainprep/doc/../brainprep/resources/MNI152_T1_1mm_b
rain.nii.gz
[info] - setting workspace directory:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669
[command] - brainprep interface reorient -image-file
/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_T1w.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/01-reorient -entities sub-02_modality-T1w_mod-T1w_ses-01_run-21669 -verbose
True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.reorient(
    image_file=PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_
T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_21669/01-reorient'),
    entities={'sub': '02', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'21669'},
)
[command] - fslreorient2std
/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_T1w.nii.gz
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/01-reorient/sub-02_ses-01_run-21669_mod-T1w_reorient.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/01-reorient/sub-02_ses-01_run-21669_mod-T1w_reorient.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface brainmask -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/01-reorient/sub-02_ses-01_run-21669_mod-T1w_reorient.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/02-brainmask -entities sub-02_modality-T1w_mod-T1w_ses-01_run-21669 -verbose
True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.brainmask(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_21669/01-reorient/sub-02_ses-01_run-21669_mod-T1w_reorie
nt.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_21669/02-brainmask'),
    entities={'sub': '02', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'21669'},
)
[command] - mri_synthstrip -i
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/01-reorient/sub-02_ses-01_run-21669_mod-T1w_reorient.nii.gz -o
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/02-brainmask/sub-02_ses-01_run-21669_mod-T1w_brain.nii.gz -m
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/02-brainmask/sub-02_ses-01_run-21669_mod-T1w_brainmask.nii.gz -f 0 --no-csf
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/02-brainmask/sub-02_ses-01_run-21669_mod-T1w_brain.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/02-brainmask/sub-02_ses-01_run-21669_mod-T1w_brainmask.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface biasfield -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/01-reorient/sub-02_ses-01_run-21669_mod-T1w_reorient.nii.gz -mask-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/02-brainmask/sub-02_ses-01_run-21669_mod-T1w_brainmask.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/03-biasfield -entities sub-02_modality-T1w_mod-T1w_ses-01_run-21669 -quick
False -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.ants.biasfield(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_21669/01-reorient/sub-02_ses-01_run-21669_mod-T1w_reorie
nt.nii.gz'),
    mask_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/s
ub-02/ses-01/workspace_21669/02-brainmask/sub-02_ses-01_run-21669_mod-T1w_brainm
ask.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_21669/03-biasfield'),
    entities={'sub': '02', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'21669'},
    quick=False,
)
[command] - N4BiasFieldCorrection -d 3 -i
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/01-reorient/sub-02_ses-01_run-21669_mod-T1w_reorient.nii.gz -s 1 -b
[1x1x1,3] -c [50x50x50x50,0.001] -t [0.15,0.01,200] -x
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/02-brainmask/sub-02_ses-01_run-21669_mod-T1w_brainmask.nii.gz -o
[/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_2
1669/03-biasfield/sub-02_ses-01_run-21669_mod-T1w_biascorrected.nii.gz,/tmp/brai
nprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21669/03-bi
asfield/sub-02_ses-01_run-21669_mod-T1w_biasfield.nii.gz] -v
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/03-biasfield/sub-02_ses-01_run-21669_mod-T1w_biascorrected.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/03-biasfield/sub-02_ses-01_run-21669_mod-T1w_biasfield.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applymask -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/03-biasfield/sub-02_ses-01_run-21669_mod-T1w_biascorrected.nii.gz -mask-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/02-brainmask/sub-02_ses-01_run-21669_mod-T1w_brainmask.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/03-biasfield -entities sub-02_modality-T1w_mod-T1w_ses-01_run-21669 -verbose
True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.applymask(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_21669/03-biasfield/sub-02_ses-01_run-21669_mod-T1w_biasc
orrected.nii.gz'),
    mask_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/s
ub-02/ses-01/workspace_21669/02-brainmask/sub-02_ses-01_run-21669_mod-T1w_brainm
ask.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_21669/03-biasfield'),
    entities={'sub': '02', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'21669'},
)
[command] - fslmaths
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/03-biasfield/sub-02_ses-01_run-21669_mod-T1w_biascorrected.nii.gz -mas
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/02-brainmask/sub-02_ses-01_run-21669_mod-T1w_brainmask.nii.gz
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/03-biasfield/sub-02_ses-01_run-21669_mod-T1w_applymask.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/03-biasfield/sub-02_ses-01_run-21669_mod-T1w_applymask.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface scale -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/03-biasfield/sub-02_ses-01_run-21669_mod-T1w_applymask.nii.gz -scale 1
-output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/04-scale -entities sub-02_modality-T1w_mod-T1w_ses-01_run-21669
-interpolation spline -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.scale(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_21669/03-biasfield/sub-02_ses-01_run-21669_mod-T1w_apply
mask.nii.gz'),
    scale=1,
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_21669/04-scale'),
    entities={'sub': '02', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'21669'},
    interpolation='spline',
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/03-biasfield/sub-02_ses-01_run-21669_mod-T1w_applymask.nii.gz -ref
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/03-biasfield/sub-02_ses-01_run-21669_mod-T1w_applymask.nii.gz -applyisoxfm 1
-interp spline -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/04-scale/sub-02_ses-01_run-21669_mod-T1w_scale.nii.gz -omat
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/04-scale/sub-02_ses-01_run-21669_mod-T1w_scale.txt -verbose 1
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/04-scale/sub-02_ses-01_run-21669_mod-T1w_scale.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/04-scale/sub-02_ses-01_run-21669_mod-T1w_scale.txt
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface affine -anatomical-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/04-scale/sub-02_ses-01_run-21669_mod-T1w_scale.nii.gz -template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T1_1mm_brain.ni
i.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/05-affine -entities sub-02_modality-T1w_mod-T1w_ses-01_run-21669 -rigid
False -quick False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.affine(
    anatomical_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subj
ects/sub-02/ses-01/workspace_21669/04-scale/sub-02_ses-01_run-21669_mod-T1w_scal
e.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T1_1mm_brain.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_21669/05-affine'),
    entities={'sub': '02', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'21669'},
    rigid=False,
    quick=False,
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/04-scale/sub-02_ses-01_run-21669_mod-T1w_scale.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T1_1mm_brain.ni
i.gz -cost normmi -searchcost normmi -anglerep euler -bins 256 -interp trilinear
-dof 9 -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/05-affine/sub-02_ses-01_run-21669_mod-T1w_affine.nii.gz -omat
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/05-affine/sub-02_ses-01_run-21669_mod-T1w_affine.txt -verbose 1
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/05-affine/sub-02_ses-01_run-21669_mod-T1w_affine.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/05-affine/sub-02_ses-01_run-21669_mod-T1w_affine.txt
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applyaffine -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/03-biasfield/sub-02_ses-01_run-21669_mod-T1w_biascorrected.nii.gz
-template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T1_1mm_brain.ni
i.gz -transform-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/05-affine/sub-02_ses-01_run-21669_mod-T1w_affine.txt -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/06-applyaffine -entities sub-02_modality-T1w_mod-T1w_ses-01_run-21669
-interpolation spline -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.applyaffine(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_21669/03-biasfield/sub-02_ses-01_run-21669_mod-T1w_biasc
orrected.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T1_1mm_brain.nii.gz'),
    transform_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subje
cts/sub-02/ses-01/workspace_21669/05-affine/sub-02_ses-01_run-21669_mod-T1w_affi
ne.txt'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_21669/06-applyaffine'),
    entities={'sub': '02', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'21669'},
    interpolation='spline',
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/03-biasfield/sub-02_ses-01_run-21669_mod-T1w_biascorrected.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T1_1mm_brain.ni
i.gz -init
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/05-affine/sub-02_ses-01_run-21669_mod-T1w_affine.txt -interp spline
-applyxfm -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/06-applyaffine/sub-02_ses-01_run-21669_mod-T1w_applyaffine.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/06-applyaffine/sub-02_ses-01_run-21669_mod-T1w_applyaffine.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applyaffine -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/02-brainmask/sub-02_ses-01_run-21669_mod-T1w_brainmask.nii.gz -template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T1_1mm_brain.ni
i.gz -transform-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/05-affine/sub-02_ses-01_run-21669_mod-T1w_affine.txt -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/07-applyaffine -entities sub-02_modality-T1w_mod-T1w_ses-01_run-21669
-interpolation nearestneighbour -verbose True -dryrun True -no-color False
-skip-run-check False -cat12-file /opt/cat12/standalone/cat_standalone.sh
-spm12-dir /opt/cat12 -matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.applyaffine(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_21669/02-brainmask/sub-02_ses-01_run-21669_mod-T1w_brain
mask.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T1_1mm_brain.nii.gz'),
    transform_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subje
cts/sub-02/ses-01/workspace_21669/05-affine/sub-02_ses-01_run-21669_mod-T1w_affi
ne.txt'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_21669/07-applyaffine'),
    entities={'sub': '02', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'21669'},
    interpolation='nearestneighbour',
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/02-brainmask/sub-02_ses-01_run-21669_mod-T1w_brainmask.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T1_1mm_brain.ni
i.gz -init
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/05-affine/sub-02_ses-01_run-21669_mod-T1w_affine.txt -interp
nearestneighbour -applyxfm -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/07-applyaffine/sub-02_ses-01_run-21669_mod-T1w_applyaffine.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/07-applyaffine/sub-02_ses-01_run-21669_mod-T1w_applyaffine.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface copyfiles -source-files
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21
669/06-applyaffine/sub-02_ses-01_run-21669_mod-T1w_applyaffine.nii.gz,/tmp/brain
prep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21669/07-app
lyaffine/sub-02_ses-01_run-21669_mod-T1w_applyaffine.nii.gz,/tmp/brainprep-quasi
raw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_21669/05-affine/sub-02
_ses-01_run-21669_mod-T1w_affine.txt -destination-files
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/sub-02_ses-0
1_run-21669_T1w.nii.gz,/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub
-02/ses-01/sub-02_ses-01_run-21669_mod-T1w_brainmask.nii.gz,/tmp/brainprep-quasi
raw/derivatives/quasiraw/subjects/sub-02/ses-01/sub-02_ses-01_run-21669_mod-T1w_
affine.txt -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01 -move-files
False -dryrun False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.utils.copyfiles(
    source_files=[PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjec
ts/sub-02/ses-01/workspace_21669/06-applyaffine/sub-02_ses-01_run-21669_mod-T1w_
applyaffine.nii.gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/w
orkspace_21669/07-applyaffine/sub-02_ses-01_run-21669_mod-T1w_applyaffine.nii.gz
'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/w
orkspace_21669/05-affine/sub-02_ses-01_run-21669_mod-T1w_affine.txt')],
    destination_files=[PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/s
ubjects/sub-02/ses-01/sub-02_ses-01_run-21669_T1w.nii.gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/s
ub-02_ses-01_run-21669_mod-T1w_brainmask.nii.gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/s
ub-02_ses-01_run-21669_mod-T1w_affine.txt')],
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01'),
    move_files=False,
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[title] - Subject Level Quasi-RAW done.
__________________________________________________________________0.08s, 0.00min
[title] - Group Level Quasi-RAW...
________________________________________________________________________________
[call] brainprep.workflow.quasiraw.brainprep_group_quasiraw(
    modality='T1w',
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw'),
    correlation_threshold=0.5,
    keep_intermediate=False,
)
[info] - setting template file:
/home/runner/work/brainprep/brainprep/doc/../brainprep/resources/MNI152_T1_1mm_b
rain.nii.gz
[command] - brainprep interface mean-correlation -data-files-regex
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-*/ses-*/*_T1w.nii.gz
-atlas-file
/home/runner/work/brainprep/brainprep/doc/../brainprep/resources/MNI152_T1_1mm_b
rain.nii.gz -output-dir /tmp/brainprep-quasiraw/derivatives/quasiraw
-correlation-threshold 0.5 -suffix _T1w -dryrun False -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.qualcheck.mean_correlation(
    data_files_regex=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/sub
jects/sub-*/ses-*/*_T1w.nii.gz'),
    atlas_file=PosixPath('/home/runner/work/brainprep/brainprep/doc/../brainprep
/resources/MNI152_T1_1mm_brain.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_c
heck'),
    correlation_threshold=0.5,
    suffix='_T1w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_check/mean_correlations_T1w
.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-histogram -table-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_check/mean_correlations_T1w
.tsv -col-name mean_correlation -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw -bar-coords 0.5 -suffix _T1w
-dryrun False -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.plotting.plot_histogram(
    table_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_c
heck/mean_correlations_T1w.tsv'),
    col_name='mean_correlation',
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/figures')
,
    bar_coords=[0.5],
    suffix='_T1w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/figures/histogram_mean_correlation_
T1w.png
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface incremental-pca -image-files-regex
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-*/ses-*/*_T1w.nii.gz
-output-dir /tmp/brainprep-quasiraw/derivatives/quasiraw -batch-size 50 -suffix
_T1w -dryrun False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.qualcheck.incremental_pca(
    image_files_regex=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/su
bjects/sub-*/ses-*/*_T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_c
heck'),
    batch_size=50,
    suffix='_T1w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_check/pca_T1w.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-pca -pca-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_check/pca_T1w.tsv
-output-dir /tmp/brainprep-quasiraw/derivatives/quasiraw -suffix _T1w -dryrun
False -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.plotting.plot_pca(
    pca_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_che
ck/pca_T1w.tsv'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/figures')
,
    suffix='_T1w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/figures/pca_T1w.png
__________________________________________________________________0.00s, 0.00min
[title] - Group Level Quasi-RAW done.
__________________________________________________________________0.03s, 0.00min
[warn] - BIDS file name does not contain run key: sub-01_T2w.nii.gz
[title] - Subject Level Quasi-RAW...
________________________________________________________________________________
[call] brainprep.workflow.quasiraw.brainprep_quasiraw(
    anatomical_file=PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/su
b-01_T2w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01'),
    rigid=False,
    quick=False,
    keep_intermediate=True,
    kwargs={'entities': {'sub': '01', 'modality': 'T2w', 'mod': 'T2w', 'ses':
'01', 'run': '17909'}},
)
[info] - setting template file:
/home/runner/work/brainprep/brainprep/doc/../brainprep/resources/MNI152_T2_1mm_b
rain.nii.gz
[info] - setting workspace directory:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909
[command] - brainprep interface reorient -image-file
/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_T2w.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/01-reorient -entities sub-01_modality-T2w_mod-T2w_ses-01_run-17909 -verbose
True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.reorient(
    image_file=PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_
T2w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_17909/01-reorient'),
    entities={'sub': '01', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'17909'},
)
[command] - fslreorient2std
/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_T2w.nii.gz
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/01-reorient/sub-01_ses-01_run-17909_mod-T2w_reorient.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/01-reorient/sub-01_ses-01_run-17909_mod-T2w_reorient.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface brainmask -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/01-reorient/sub-01_ses-01_run-17909_mod-T2w_reorient.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/02-brainmask -entities sub-01_modality-T2w_mod-T2w_ses-01_run-17909 -verbose
True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.brainmask(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_17909/01-reorient/sub-01_ses-01_run-17909_mod-T2w_reorie
nt.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_17909/02-brainmask'),
    entities={'sub': '01', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'17909'},
)
[command] - mri_synthstrip -i
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/01-reorient/sub-01_ses-01_run-17909_mod-T2w_reorient.nii.gz -o
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/02-brainmask/sub-01_ses-01_run-17909_mod-T2w_brain.nii.gz -m
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/02-brainmask/sub-01_ses-01_run-17909_mod-T2w_brainmask.nii.gz -f 0 --no-csf
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/02-brainmask/sub-01_ses-01_run-17909_mod-T2w_brain.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/02-brainmask/sub-01_ses-01_run-17909_mod-T2w_brainmask.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface biasfield -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/01-reorient/sub-01_ses-01_run-17909_mod-T2w_reorient.nii.gz -mask-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/02-brainmask/sub-01_ses-01_run-17909_mod-T2w_brainmask.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/03-biasfield -entities sub-01_modality-T2w_mod-T2w_ses-01_run-17909 -quick
False -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.ants.biasfield(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_17909/01-reorient/sub-01_ses-01_run-17909_mod-T2w_reorie
nt.nii.gz'),
    mask_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/s
ub-01/ses-01/workspace_17909/02-brainmask/sub-01_ses-01_run-17909_mod-T2w_brainm
ask.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_17909/03-biasfield'),
    entities={'sub': '01', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'17909'},
    quick=False,
)
[command] - N4BiasFieldCorrection -d 3 -i
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/01-reorient/sub-01_ses-01_run-17909_mod-T2w_reorient.nii.gz -s 1 -b
[1x1x1,3] -c [50x50x50x50,0.001] -t [0.15,0.01,200] -x
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/02-brainmask/sub-01_ses-01_run-17909_mod-T2w_brainmask.nii.gz -o
[/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_1
7909/03-biasfield/sub-01_ses-01_run-17909_mod-T2w_biascorrected.nii.gz,/tmp/brai
nprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17909/03-bi
asfield/sub-01_ses-01_run-17909_mod-T2w_biasfield.nii.gz] -v
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/03-biasfield/sub-01_ses-01_run-17909_mod-T2w_biascorrected.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/03-biasfield/sub-01_ses-01_run-17909_mod-T2w_biasfield.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applymask -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/03-biasfield/sub-01_ses-01_run-17909_mod-T2w_biascorrected.nii.gz -mask-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/02-brainmask/sub-01_ses-01_run-17909_mod-T2w_brainmask.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/03-biasfield -entities sub-01_modality-T2w_mod-T2w_ses-01_run-17909 -verbose
True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.applymask(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_17909/03-biasfield/sub-01_ses-01_run-17909_mod-T2w_biasc
orrected.nii.gz'),
    mask_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/s
ub-01/ses-01/workspace_17909/02-brainmask/sub-01_ses-01_run-17909_mod-T2w_brainm
ask.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_17909/03-biasfield'),
    entities={'sub': '01', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'17909'},
)
[command] - fslmaths
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/03-biasfield/sub-01_ses-01_run-17909_mod-T2w_biascorrected.nii.gz -mas
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/02-brainmask/sub-01_ses-01_run-17909_mod-T2w_brainmask.nii.gz
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/03-biasfield/sub-01_ses-01_run-17909_mod-T2w_applymask.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/03-biasfield/sub-01_ses-01_run-17909_mod-T2w_applymask.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface scale -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/03-biasfield/sub-01_ses-01_run-17909_mod-T2w_applymask.nii.gz -scale 1
-output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/04-scale -entities sub-01_modality-T2w_mod-T2w_ses-01_run-17909
-interpolation spline -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.scale(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_17909/03-biasfield/sub-01_ses-01_run-17909_mod-T2w_apply
mask.nii.gz'),
    scale=1,
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_17909/04-scale'),
    entities={'sub': '01', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'17909'},
    interpolation='spline',
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/03-biasfield/sub-01_ses-01_run-17909_mod-T2w_applymask.nii.gz -ref
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/03-biasfield/sub-01_ses-01_run-17909_mod-T2w_applymask.nii.gz -applyisoxfm 1
-interp spline -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/04-scale/sub-01_ses-01_run-17909_mod-T2w_scale.nii.gz -omat
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/04-scale/sub-01_ses-01_run-17909_mod-T2w_scale.txt -verbose 1
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/04-scale/sub-01_ses-01_run-17909_mod-T2w_scale.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/04-scale/sub-01_ses-01_run-17909_mod-T2w_scale.txt
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface affine -anatomical-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/04-scale/sub-01_ses-01_run-17909_mod-T2w_scale.nii.gz -template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/05-affine -entities sub-01_modality-T2w_mod-T2w_ses-01_run-17909 -rigid
False -quick False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.affine(
    anatomical_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subj
ects/sub-01/ses-01/workspace_17909/04-scale/sub-01_ses-01_run-17909_mod-T2w_scal
e.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T2_1mm_brain.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_17909/05-affine'),
    entities={'sub': '01', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'17909'},
    rigid=False,
    quick=False,
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/04-scale/sub-01_ses-01_run-17909_mod-T2w_scale.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -cost normmi -searchcost normmi -anglerep euler -bins 256 -interp trilinear
-dof 9 -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/05-affine/sub-01_ses-01_run-17909_mod-T2w_affine.nii.gz -omat
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/05-affine/sub-01_ses-01_run-17909_mod-T2w_affine.txt -verbose 1
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/05-affine/sub-01_ses-01_run-17909_mod-T2w_affine.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/05-affine/sub-01_ses-01_run-17909_mod-T2w_affine.txt
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applyaffine -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/03-biasfield/sub-01_ses-01_run-17909_mod-T2w_biascorrected.nii.gz
-template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -transform-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/05-affine/sub-01_ses-01_run-17909_mod-T2w_affine.txt -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/06-applyaffine -entities sub-01_modality-T2w_mod-T2w_ses-01_run-17909
-interpolation spline -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.applyaffine(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_17909/03-biasfield/sub-01_ses-01_run-17909_mod-T2w_biasc
orrected.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T2_1mm_brain.nii.gz'),
    transform_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subje
cts/sub-01/ses-01/workspace_17909/05-affine/sub-01_ses-01_run-17909_mod-T2w_affi
ne.txt'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_17909/06-applyaffine'),
    entities={'sub': '01', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'17909'},
    interpolation='spline',
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/03-biasfield/sub-01_ses-01_run-17909_mod-T2w_biascorrected.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -init
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/05-affine/sub-01_ses-01_run-17909_mod-T2w_affine.txt -interp spline
-applyxfm -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/06-applyaffine/sub-01_ses-01_run-17909_mod-T2w_applyaffine.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/06-applyaffine/sub-01_ses-01_run-17909_mod-T2w_applyaffine.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applyaffine -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/02-brainmask/sub-01_ses-01_run-17909_mod-T2w_brainmask.nii.gz -template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -transform-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/05-affine/sub-01_ses-01_run-17909_mod-T2w_affine.txt -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/07-applyaffine -entities sub-01_modality-T2w_mod-T2w_ses-01_run-17909
-interpolation nearestneighbour -verbose True -dryrun True -no-color False
-skip-run-check False -cat12-file /opt/cat12/standalone/cat_standalone.sh
-spm12-dir /opt/cat12 -matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.applyaffine(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_17909/02-brainmask/sub-01_ses-01_run-17909_mod-T2w_brain
mask.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T2_1mm_brain.nii.gz'),
    transform_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subje
cts/sub-01/ses-01/workspace_17909/05-affine/sub-01_ses-01_run-17909_mod-T2w_affi
ne.txt'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_17909/07-applyaffine'),
    entities={'sub': '01', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'17909'},
    interpolation='nearestneighbour',
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/02-brainmask/sub-01_ses-01_run-17909_mod-T2w_brainmask.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -init
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/05-affine/sub-01_ses-01_run-17909_mod-T2w_affine.txt -interp
nearestneighbour -applyxfm -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/07-applyaffine/sub-01_ses-01_run-17909_mod-T2w_applyaffine.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/07-applyaffine/sub-01_ses-01_run-17909_mod-T2w_applyaffine.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface copyfiles -source-files
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17
909/06-applyaffine/sub-01_ses-01_run-17909_mod-T2w_applyaffine.nii.gz,/tmp/brain
prep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17909/07-app
lyaffine/sub-01_ses-01_run-17909_mod-T2w_applyaffine.nii.gz,/tmp/brainprep-quasi
raw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_17909/05-affine/sub-01
_ses-01_run-17909_mod-T2w_affine.txt -destination-files
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/sub-01_ses-0
1_run-17909_T2w.nii.gz,/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub
-01/ses-01/sub-01_ses-01_run-17909_mod-T2w_brainmask.nii.gz,/tmp/brainprep-quasi
raw/derivatives/quasiraw/subjects/sub-01/ses-01/sub-01_ses-01_run-17909_mod-T2w_
affine.txt -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01 -move-files
False -dryrun False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.utils.copyfiles(
    source_files=[PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjec
ts/sub-01/ses-01/workspace_17909/06-applyaffine/sub-01_ses-01_run-17909_mod-T2w_
applyaffine.nii.gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/w
orkspace_17909/07-applyaffine/sub-01_ses-01_run-17909_mod-T2w_applyaffine.nii.gz
'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/w
orkspace_17909/05-affine/sub-01_ses-01_run-17909_mod-T2w_affine.txt')],
    destination_files=[PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/s
ubjects/sub-01/ses-01/sub-01_ses-01_run-17909_T2w.nii.gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/s
ub-01_ses-01_run-17909_mod-T2w_brainmask.nii.gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/s
ub-01_ses-01_run-17909_mod-T2w_affine.txt')],
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01'),
    move_files=False,
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[title] - Subject Level Quasi-RAW done.
__________________________________________________________________0.09s, 0.00min
[warn] - BIDS file name does not contain run key: sub-02_T2w.nii.gz
[title] - Subject Level Quasi-RAW...
________________________________________________________________________________
[call] brainprep.workflow.quasiraw.brainprep_quasiraw(
    anatomical_file=PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/su
b-02_T2w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01'),
    rigid=False,
    quick=False,
    keep_intermediate=True,
    kwargs={'entities': {'sub': '02', 'modality': 'T2w', 'mod': 'T2w', 'ses':
'01', 'run': '32679'}},
)
[info] - setting template file:
/home/runner/work/brainprep/brainprep/doc/../brainprep/resources/MNI152_T2_1mm_b
rain.nii.gz
[info] - setting workspace directory:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679
[command] - brainprep interface reorient -image-file
/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_T2w.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/01-reorient -entities sub-02_modality-T2w_mod-T2w_ses-01_run-32679 -verbose
True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.reorient(
    image_file=PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_
T2w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_32679/01-reorient'),
    entities={'sub': '02', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'32679'},
)
[command] - fslreorient2std
/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_T2w.nii.gz
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/01-reorient/sub-02_ses-01_run-32679_mod-T2w_reorient.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/01-reorient/sub-02_ses-01_run-32679_mod-T2w_reorient.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface brainmask -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/01-reorient/sub-02_ses-01_run-32679_mod-T2w_reorient.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/02-brainmask -entities sub-02_modality-T2w_mod-T2w_ses-01_run-32679 -verbose
True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.brainmask(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_32679/01-reorient/sub-02_ses-01_run-32679_mod-T2w_reorie
nt.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_32679/02-brainmask'),
    entities={'sub': '02', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'32679'},
)
[command] - mri_synthstrip -i
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/01-reorient/sub-02_ses-01_run-32679_mod-T2w_reorient.nii.gz -o
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/02-brainmask/sub-02_ses-01_run-32679_mod-T2w_brain.nii.gz -m
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/02-brainmask/sub-02_ses-01_run-32679_mod-T2w_brainmask.nii.gz -f 0 --no-csf
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/02-brainmask/sub-02_ses-01_run-32679_mod-T2w_brain.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/02-brainmask/sub-02_ses-01_run-32679_mod-T2w_brainmask.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface biasfield -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/01-reorient/sub-02_ses-01_run-32679_mod-T2w_reorient.nii.gz -mask-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/02-brainmask/sub-02_ses-01_run-32679_mod-T2w_brainmask.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/03-biasfield -entities sub-02_modality-T2w_mod-T2w_ses-01_run-32679 -quick
False -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.ants.biasfield(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_32679/01-reorient/sub-02_ses-01_run-32679_mod-T2w_reorie
nt.nii.gz'),
    mask_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/s
ub-02/ses-01/workspace_32679/02-brainmask/sub-02_ses-01_run-32679_mod-T2w_brainm
ask.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_32679/03-biasfield'),
    entities={'sub': '02', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'32679'},
    quick=False,
)
[command] - N4BiasFieldCorrection -d 3 -i
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/01-reorient/sub-02_ses-01_run-32679_mod-T2w_reorient.nii.gz -s 1 -b
[1x1x1,3] -c [50x50x50x50,0.001] -t [0.15,0.01,200] -x
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/02-brainmask/sub-02_ses-01_run-32679_mod-T2w_brainmask.nii.gz -o
[/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_3
2679/03-biasfield/sub-02_ses-01_run-32679_mod-T2w_biascorrected.nii.gz,/tmp/brai
nprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32679/03-bi
asfield/sub-02_ses-01_run-32679_mod-T2w_biasfield.nii.gz] -v
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/03-biasfield/sub-02_ses-01_run-32679_mod-T2w_biascorrected.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/03-biasfield/sub-02_ses-01_run-32679_mod-T2w_biasfield.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applymask -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/03-biasfield/sub-02_ses-01_run-32679_mod-T2w_biascorrected.nii.gz -mask-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/02-brainmask/sub-02_ses-01_run-32679_mod-T2w_brainmask.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/03-biasfield -entities sub-02_modality-T2w_mod-T2w_ses-01_run-32679 -verbose
True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.applymask(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_32679/03-biasfield/sub-02_ses-01_run-32679_mod-T2w_biasc
orrected.nii.gz'),
    mask_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/s
ub-02/ses-01/workspace_32679/02-brainmask/sub-02_ses-01_run-32679_mod-T2w_brainm
ask.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_32679/03-biasfield'),
    entities={'sub': '02', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'32679'},
)
[command] - fslmaths
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/03-biasfield/sub-02_ses-01_run-32679_mod-T2w_biascorrected.nii.gz -mas
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/02-brainmask/sub-02_ses-01_run-32679_mod-T2w_brainmask.nii.gz
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/03-biasfield/sub-02_ses-01_run-32679_mod-T2w_applymask.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/03-biasfield/sub-02_ses-01_run-32679_mod-T2w_applymask.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface scale -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/03-biasfield/sub-02_ses-01_run-32679_mod-T2w_applymask.nii.gz -scale 1
-output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/04-scale -entities sub-02_modality-T2w_mod-T2w_ses-01_run-32679
-interpolation spline -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.scale(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_32679/03-biasfield/sub-02_ses-01_run-32679_mod-T2w_apply
mask.nii.gz'),
    scale=1,
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_32679/04-scale'),
    entities={'sub': '02', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'32679'},
    interpolation='spline',
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/03-biasfield/sub-02_ses-01_run-32679_mod-T2w_applymask.nii.gz -ref
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/03-biasfield/sub-02_ses-01_run-32679_mod-T2w_applymask.nii.gz -applyisoxfm 1
-interp spline -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/04-scale/sub-02_ses-01_run-32679_mod-T2w_scale.nii.gz -omat
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/04-scale/sub-02_ses-01_run-32679_mod-T2w_scale.txt -verbose 1
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/04-scale/sub-02_ses-01_run-32679_mod-T2w_scale.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/04-scale/sub-02_ses-01_run-32679_mod-T2w_scale.txt
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface affine -anatomical-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/04-scale/sub-02_ses-01_run-32679_mod-T2w_scale.nii.gz -template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/05-affine -entities sub-02_modality-T2w_mod-T2w_ses-01_run-32679 -rigid
False -quick False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.affine(
    anatomical_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subj
ects/sub-02/ses-01/workspace_32679/04-scale/sub-02_ses-01_run-32679_mod-T2w_scal
e.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T2_1mm_brain.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_32679/05-affine'),
    entities={'sub': '02', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'32679'},
    rigid=False,
    quick=False,
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/04-scale/sub-02_ses-01_run-32679_mod-T2w_scale.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -cost normmi -searchcost normmi -anglerep euler -bins 256 -interp trilinear
-dof 9 -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/05-affine/sub-02_ses-01_run-32679_mod-T2w_affine.nii.gz -omat
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/05-affine/sub-02_ses-01_run-32679_mod-T2w_affine.txt -verbose 1
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/05-affine/sub-02_ses-01_run-32679_mod-T2w_affine.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/05-affine/sub-02_ses-01_run-32679_mod-T2w_affine.txt
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applyaffine -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/03-biasfield/sub-02_ses-01_run-32679_mod-T2w_biascorrected.nii.gz
-template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -transform-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/05-affine/sub-02_ses-01_run-32679_mod-T2w_affine.txt -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/06-applyaffine -entities sub-02_modality-T2w_mod-T2w_ses-01_run-32679
-interpolation spline -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.applyaffine(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_32679/03-biasfield/sub-02_ses-01_run-32679_mod-T2w_biasc
orrected.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T2_1mm_brain.nii.gz'),
    transform_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subje
cts/sub-02/ses-01/workspace_32679/05-affine/sub-02_ses-01_run-32679_mod-T2w_affi
ne.txt'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_32679/06-applyaffine'),
    entities={'sub': '02', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'32679'},
    interpolation='spline',
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/03-biasfield/sub-02_ses-01_run-32679_mod-T2w_biascorrected.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -init
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/05-affine/sub-02_ses-01_run-32679_mod-T2w_affine.txt -interp spline
-applyxfm -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/06-applyaffine/sub-02_ses-01_run-32679_mod-T2w_applyaffine.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/06-applyaffine/sub-02_ses-01_run-32679_mod-T2w_applyaffine.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applyaffine -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/02-brainmask/sub-02_ses-01_run-32679_mod-T2w_brainmask.nii.gz -template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -transform-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/05-affine/sub-02_ses-01_run-32679_mod-T2w_affine.txt -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/07-applyaffine -entities sub-02_modality-T2w_mod-T2w_ses-01_run-32679
-interpolation nearestneighbour -verbose True -dryrun True -no-color False
-skip-run-check False -cat12-file /opt/cat12/standalone/cat_standalone.sh
-spm12-dir /opt/cat12 -matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.applyaffine(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_32679/02-brainmask/sub-02_ses-01_run-32679_mod-T2w_brain
mask.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T2_1mm_brain.nii.gz'),
    transform_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subje
cts/sub-02/ses-01/workspace_32679/05-affine/sub-02_ses-01_run-32679_mod-T2w_affi
ne.txt'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_32679/07-applyaffine'),
    entities={'sub': '02', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'32679'},
    interpolation='nearestneighbour',
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/02-brainmask/sub-02_ses-01_run-32679_mod-T2w_brainmask.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -init
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/05-affine/sub-02_ses-01_run-32679_mod-T2w_affine.txt -interp
nearestneighbour -applyxfm -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/07-applyaffine/sub-02_ses-01_run-32679_mod-T2w_applyaffine.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/07-applyaffine/sub-02_ses-01_run-32679_mod-T2w_applyaffine.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface copyfiles -source-files
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32
679/06-applyaffine/sub-02_ses-01_run-32679_mod-T2w_applyaffine.nii.gz,/tmp/brain
prep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32679/07-app
lyaffine/sub-02_ses-01_run-32679_mod-T2w_applyaffine.nii.gz,/tmp/brainprep-quasi
raw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_32679/05-affine/sub-02
_ses-01_run-32679_mod-T2w_affine.txt -destination-files
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/sub-02_ses-0
1_run-32679_T2w.nii.gz,/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub
-02/ses-01/sub-02_ses-01_run-32679_mod-T2w_brainmask.nii.gz,/tmp/brainprep-quasi
raw/derivatives/quasiraw/subjects/sub-02/ses-01/sub-02_ses-01_run-32679_mod-T2w_
affine.txt -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01 -move-files
False -dryrun False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.utils.copyfiles(
    source_files=[PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjec
ts/sub-02/ses-01/workspace_32679/06-applyaffine/sub-02_ses-01_run-32679_mod-T2w_
applyaffine.nii.gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/w
orkspace_32679/07-applyaffine/sub-02_ses-01_run-32679_mod-T2w_applyaffine.nii.gz
'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/w
orkspace_32679/05-affine/sub-02_ses-01_run-32679_mod-T2w_affine.txt')],
    destination_files=[PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/s
ubjects/sub-02/ses-01/sub-02_ses-01_run-32679_T2w.nii.gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/s
ub-02_ses-01_run-32679_mod-T2w_brainmask.nii.gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/s
ub-02_ses-01_run-32679_mod-T2w_affine.txt')],
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01'),
    move_files=False,
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[title] - Subject Level Quasi-RAW done.
__________________________________________________________________0.08s, 0.00min
[title] - Group Level Quasi-RAW...
________________________________________________________________________________
[call] brainprep.workflow.quasiraw.brainprep_group_quasiraw(
    modality='T2w',
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw'),
    correlation_threshold=0.5,
    keep_intermediate=False,
)
[info] - setting template file:
/home/runner/work/brainprep/brainprep/doc/../brainprep/resources/MNI152_T2_1mm_b
rain.nii.gz
[command] - brainprep interface mean-correlation -data-files-regex
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-*/ses-*/*_T2w.nii.gz
-atlas-file
/home/runner/work/brainprep/brainprep/doc/../brainprep/resources/MNI152_T2_1mm_b
rain.nii.gz -output-dir /tmp/brainprep-quasiraw/derivatives/quasiraw
-correlation-threshold 0.5 -suffix _T2w -dryrun False -verbose True -dryrun True
-no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.qualcheck.mean_correlation(
    data_files_regex=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/sub
jects/sub-*/ses-*/*_T2w.nii.gz'),
    atlas_file=PosixPath('/home/runner/work/brainprep/brainprep/doc/../brainprep
/resources/MNI152_T2_1mm_brain.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_c
heck'),
    correlation_threshold=0.5,
    suffix='_T2w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_check/mean_correlations_T2w
.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-histogram -table-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_check/mean_correlations_T2w
.tsv -col-name mean_correlation -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw -bar-coords 0.5 -suffix _T2w
-dryrun False -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.plotting.plot_histogram(
    table_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_c
heck/mean_correlations_T2w.tsv'),
    col_name='mean_correlation',
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/figures')
,
    bar_coords=[0.5],
    suffix='_T2w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/figures/histogram_mean_correlation_
T2w.png
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface incremental-pca -image-files-regex
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-*/ses-*/*_T2w.nii.gz
-output-dir /tmp/brainprep-quasiraw/derivatives/quasiraw -batch-size 50 -suffix
_T2w -dryrun False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.qualcheck.incremental_pca(
    image_files_regex=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/su
bjects/sub-*/ses-*/*_T2w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_c
heck'),
    batch_size=50,
    suffix='_T2w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_check/pca_T2w.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-pca -pca-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_check/pca_T2w.tsv
-output-dir /tmp/brainprep-quasiraw/derivatives/quasiraw -suffix _T2w -dryrun
False -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.plotting.plot_pca(
    pca_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_che
ck/pca_T2w.tsv'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/figures')
,
    suffix='_T2w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/figures/pca_T2w.png
__________________________________________________________________0.00s, 0.00min
[title] - Group Level Quasi-RAW done.
__________________________________________________________________0.03s, 0.00min
[warn] - BIDS file name does not contain run key: sub-01_FLAIR.nii.gz
[title] - Subject Level Quasi-RAW...
________________________________________________________________________________
[call] brainprep.workflow.quasiraw.brainprep_quasiraw(
    anatomical_file=PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/su
b-01_FLAIR.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01'),
    rigid=False,
    quick=False,
    keep_intermediate=True,
    kwargs={'entities': {'sub': '01', 'modality': 'FLAIR', 'mod': 'FLAIR',
'ses': '01', 'run': '16566'}},
)
[info] - setting template file:
/home/runner/work/brainprep/brainprep/doc/../brainprep/resources/MNI152_T2_1mm_b
rain.nii.gz
[info] - setting workspace directory:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566
[command] - brainprep interface reorient -image-file
/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_FLAIR.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/01-reorient -entities sub-01_modality-FLAIR_mod-FLAIR_ses-01_run-16566
-verbose True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.reorient(
    image_file=PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_
FLAIR.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_16566/01-reorient'),
    entities={'sub': '01', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '16566'},
)
[command] - fslreorient2std
/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_FLAIR.nii.gz
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/01-reorient/sub-01_ses-01_run-16566_mod-FLAIR_reorient.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/01-reorient/sub-01_ses-01_run-16566_mod-FLAIR_reorient.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface brainmask -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/01-reorient/sub-01_ses-01_run-16566_mod-FLAIR_reorient.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/02-brainmask -entities sub-01_modality-FLAIR_mod-FLAIR_ses-01_run-16566
-verbose True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.brainmask(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_16566/01-reorient/sub-01_ses-01_run-16566_mod-FLAIR_reor
ient.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_16566/02-brainmask'),
    entities={'sub': '01', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '16566'},
)
[command] - mri_synthstrip -i
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/01-reorient/sub-01_ses-01_run-16566_mod-FLAIR_reorient.nii.gz -o
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/02-brainmask/sub-01_ses-01_run-16566_mod-FLAIR_brain.nii.gz -m
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/02-brainmask/sub-01_ses-01_run-16566_mod-FLAIR_brainmask.nii.gz -f 0
--no-csf
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/02-brainmask/sub-01_ses-01_run-16566_mod-FLAIR_brain.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/02-brainmask/sub-01_ses-01_run-16566_mod-FLAIR_brainmask.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface biasfield -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/01-reorient/sub-01_ses-01_run-16566_mod-FLAIR_reorient.nii.gz -mask-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/02-brainmask/sub-01_ses-01_run-16566_mod-FLAIR_brainmask.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/03-biasfield -entities sub-01_modality-FLAIR_mod-FLAIR_ses-01_run-16566
-quick False -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.ants.biasfield(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_16566/01-reorient/sub-01_ses-01_run-16566_mod-FLAIR_reor
ient.nii.gz'),
    mask_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/s
ub-01/ses-01/workspace_16566/02-brainmask/sub-01_ses-01_run-16566_mod-FLAIR_brai
nmask.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_16566/03-biasfield'),
    entities={'sub': '01', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '16566'},
    quick=False,
)
[command] - N4BiasFieldCorrection -d 3 -i
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/01-reorient/sub-01_ses-01_run-16566_mod-FLAIR_reorient.nii.gz -s 1 -b
[1x1x1,3] -c [50x50x50x50,0.001] -t [0.15,0.01,200] -x
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/02-brainmask/sub-01_ses-01_run-16566_mod-FLAIR_brainmask.nii.gz -o
[/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_1
6566/03-biasfield/sub-01_ses-01_run-16566_mod-FLAIR_biascorrected.nii.gz,/tmp/br
ainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16566/03-
biasfield/sub-01_ses-01_run-16566_mod-FLAIR_biasfield.nii.gz] -v
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/03-biasfield/sub-01_ses-01_run-16566_mod-FLAIR_biascorrected.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/03-biasfield/sub-01_ses-01_run-16566_mod-FLAIR_biasfield.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applymask -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/03-biasfield/sub-01_ses-01_run-16566_mod-FLAIR_biascorrected.nii.gz
-mask-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/02-brainmask/sub-01_ses-01_run-16566_mod-FLAIR_brainmask.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/03-biasfield -entities sub-01_modality-FLAIR_mod-FLAIR_ses-01_run-16566
-verbose True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.applymask(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_16566/03-biasfield/sub-01_ses-01_run-16566_mod-FLAIR_bia
scorrected.nii.gz'),
    mask_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/s
ub-01/ses-01/workspace_16566/02-brainmask/sub-01_ses-01_run-16566_mod-FLAIR_brai
nmask.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_16566/03-biasfield'),
    entities={'sub': '01', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '16566'},
)
[command] - fslmaths
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/03-biasfield/sub-01_ses-01_run-16566_mod-FLAIR_biascorrected.nii.gz -mas
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/02-brainmask/sub-01_ses-01_run-16566_mod-FLAIR_brainmask.nii.gz
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/03-biasfield/sub-01_ses-01_run-16566_mod-FLAIR_applymask.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/03-biasfield/sub-01_ses-01_run-16566_mod-FLAIR_applymask.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface scale -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/03-biasfield/sub-01_ses-01_run-16566_mod-FLAIR_applymask.nii.gz -scale 1
-output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/04-scale -entities sub-01_modality-FLAIR_mod-FLAIR_ses-01_run-16566
-interpolation spline -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.scale(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_16566/03-biasfield/sub-01_ses-01_run-16566_mod-FLAIR_app
lymask.nii.gz'),
    scale=1,
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_16566/04-scale'),
    entities={'sub': '01', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '16566'},
    interpolation='spline',
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/03-biasfield/sub-01_ses-01_run-16566_mod-FLAIR_applymask.nii.gz -ref
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/03-biasfield/sub-01_ses-01_run-16566_mod-FLAIR_applymask.nii.gz -applyisoxfm
1 -interp spline -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/04-scale/sub-01_ses-01_run-16566_mod-FLAIR_scale.nii.gz -omat
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/04-scale/sub-01_ses-01_run-16566_mod-FLAIR_scale.txt -verbose 1
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/04-scale/sub-01_ses-01_run-16566_mod-FLAIR_scale.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/04-scale/sub-01_ses-01_run-16566_mod-FLAIR_scale.txt
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface affine -anatomical-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/04-scale/sub-01_ses-01_run-16566_mod-FLAIR_scale.nii.gz -template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/05-affine -entities sub-01_modality-FLAIR_mod-FLAIR_ses-01_run-16566 -rigid
False -quick False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.affine(
    anatomical_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subj
ects/sub-01/ses-01/workspace_16566/04-scale/sub-01_ses-01_run-16566_mod-FLAIR_sc
ale.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T2_1mm_brain.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_16566/05-affine'),
    entities={'sub': '01', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '16566'},
    rigid=False,
    quick=False,
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/04-scale/sub-01_ses-01_run-16566_mod-FLAIR_scale.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -cost normmi -searchcost normmi -anglerep euler -bins 256 -interp trilinear
-dof 9 -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/05-affine/sub-01_ses-01_run-16566_mod-FLAIR_affine.nii.gz -omat
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/05-affine/sub-01_ses-01_run-16566_mod-FLAIR_affine.txt -verbose 1
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/05-affine/sub-01_ses-01_run-16566_mod-FLAIR_affine.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/05-affine/sub-01_ses-01_run-16566_mod-FLAIR_affine.txt
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applyaffine -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/03-biasfield/sub-01_ses-01_run-16566_mod-FLAIR_biascorrected.nii.gz
-template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -transform-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/05-affine/sub-01_ses-01_run-16566_mod-FLAIR_affine.txt -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/06-applyaffine -entities sub-01_modality-FLAIR_mod-FLAIR_ses-01_run-16566
-interpolation spline -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.applyaffine(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_16566/03-biasfield/sub-01_ses-01_run-16566_mod-FLAIR_bia
scorrected.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T2_1mm_brain.nii.gz'),
    transform_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subje
cts/sub-01/ses-01/workspace_16566/05-affine/sub-01_ses-01_run-16566_mod-FLAIR_af
fine.txt'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_16566/06-applyaffine'),
    entities={'sub': '01', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '16566'},
    interpolation='spline',
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/03-biasfield/sub-01_ses-01_run-16566_mod-FLAIR_biascorrected.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -init
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/05-affine/sub-01_ses-01_run-16566_mod-FLAIR_affine.txt -interp spline
-applyxfm -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/06-applyaffine/sub-01_ses-01_run-16566_mod-FLAIR_applyaffine.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/06-applyaffine/sub-01_ses-01_run-16566_mod-FLAIR_applyaffine.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applyaffine -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/02-brainmask/sub-01_ses-01_run-16566_mod-FLAIR_brainmask.nii.gz
-template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -transform-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/05-affine/sub-01_ses-01_run-16566_mod-FLAIR_affine.txt -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/07-applyaffine -entities sub-01_modality-FLAIR_mod-FLAIR_ses-01_run-16566
-interpolation nearestneighbour -verbose True -dryrun True -no-color False
-skip-run-check False -cat12-file /opt/cat12/standalone/cat_standalone.sh
-spm12-dir /opt/cat12 -matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.applyaffine(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_16566/02-brainmask/sub-01_ses-01_run-16566_mod-FLAIR_bra
inmask.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T2_1mm_brain.nii.gz'),
    transform_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subje
cts/sub-01/ses-01/workspace_16566/05-affine/sub-01_ses-01_run-16566_mod-FLAIR_af
fine.txt'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01/workspace_16566/07-applyaffine'),
    entities={'sub': '01', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '16566'},
    interpolation='nearestneighbour',
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/02-brainmask/sub-01_ses-01_run-16566_mod-FLAIR_brainmask.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -init
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/05-affine/sub-01_ses-01_run-16566_mod-FLAIR_affine.txt -interp
nearestneighbour -applyxfm -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/07-applyaffine/sub-01_ses-01_run-16566_mod-FLAIR_applyaffine.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/07-applyaffine/sub-01_ses-01_run-16566_mod-FLAIR_applyaffine.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface copyfiles -source-files
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16
566/06-applyaffine/sub-01_ses-01_run-16566_mod-FLAIR_applyaffine.nii.gz,/tmp/bra
inprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16566/07-a
pplyaffine/sub-01_ses-01_run-16566_mod-FLAIR_applyaffine.nii.gz,/tmp/brainprep-q
uasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/workspace_16566/05-affine/su
b-01_ses-01_run-16566_mod-FLAIR_affine.txt -destination-files
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/sub-01_ses-0
1_run-16566_FLAIR.nii.gz,/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/s
ub-01/ses-01/sub-01_ses-01_run-16566_mod-FLAIR_brainmask.nii.gz,/tmp/brainprep-q
uasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/sub-01_ses-01_run-16566_mod-
FLAIR_affine.txt -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01 -move-files
False -dryrun False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.utils.copyfiles(
    source_files=[PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjec
ts/sub-01/ses-01/workspace_16566/06-applyaffine/sub-01_ses-01_run-16566_mod-FLAI
R_applyaffine.nii.gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/w
orkspace_16566/07-applyaffine/sub-01_ses-01_run-16566_mod-FLAIR_applyaffine.nii.
gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/w
orkspace_16566/05-affine/sub-01_ses-01_run-16566_mod-FLAIR_affine.txt')],
    destination_files=[PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/s
ubjects/sub-01/ses-01/sub-01_ses-01_run-16566_FLAIR.nii.gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/s
ub-01_ses-01_run-16566_mod-FLAIR_brainmask.nii.gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-01/ses-01/s
ub-01_ses-01_run-16566_mod-FLAIR_affine.txt')],
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-01/ses-01'),
    move_files=False,
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[title] - Subject Level Quasi-RAW done.
__________________________________________________________________0.08s, 0.00min
[warn] - BIDS file name does not contain run key: sub-02_FLAIR.nii.gz
[title] - Subject Level Quasi-RAW...
________________________________________________________________________________
[call] brainprep.workflow.quasiraw.brainprep_quasiraw(
    anatomical_file=PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/su
b-02_FLAIR.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01'),
    rigid=False,
    quick=False,
    keep_intermediate=True,
    kwargs={'entities': {'sub': '02', 'modality': 'FLAIR', 'mod': 'FLAIR',
'ses': '01', 'run': '24276'}},
)
[info] - setting template file:
/home/runner/work/brainprep/brainprep/doc/../brainprep/resources/MNI152_T2_1mm_b
rain.nii.gz
[info] - setting workspace directory:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276
[command] - brainprep interface reorient -image-file
/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_FLAIR.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/01-reorient -entities sub-02_modality-FLAIR_mod-FLAIR_ses-01_run-24276
-verbose True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.reorient(
    image_file=PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_
FLAIR.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_24276/01-reorient'),
    entities={'sub': '02', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '24276'},
)
[command] - fslreorient2std
/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_FLAIR.nii.gz
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/01-reorient/sub-02_ses-01_run-24276_mod-FLAIR_reorient.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/01-reorient/sub-02_ses-01_run-24276_mod-FLAIR_reorient.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface brainmask -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/01-reorient/sub-02_ses-01_run-24276_mod-FLAIR_reorient.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/02-brainmask -entities sub-02_modality-FLAIR_mod-FLAIR_ses-01_run-24276
-verbose True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.freesurfer.brainmask(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_24276/01-reorient/sub-02_ses-01_run-24276_mod-FLAIR_reor
ient.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_24276/02-brainmask'),
    entities={'sub': '02', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '24276'},
)
[command] - mri_synthstrip -i
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/01-reorient/sub-02_ses-01_run-24276_mod-FLAIR_reorient.nii.gz -o
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/02-brainmask/sub-02_ses-01_run-24276_mod-FLAIR_brain.nii.gz -m
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/02-brainmask/sub-02_ses-01_run-24276_mod-FLAIR_brainmask.nii.gz -f 0
--no-csf
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/02-brainmask/sub-02_ses-01_run-24276_mod-FLAIR_brain.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/02-brainmask/sub-02_ses-01_run-24276_mod-FLAIR_brainmask.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface biasfield -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/01-reorient/sub-02_ses-01_run-24276_mod-FLAIR_reorient.nii.gz -mask-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/02-brainmask/sub-02_ses-01_run-24276_mod-FLAIR_brainmask.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/03-biasfield -entities sub-02_modality-FLAIR_mod-FLAIR_ses-01_run-24276
-quick False -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.ants.biasfield(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_24276/01-reorient/sub-02_ses-01_run-24276_mod-FLAIR_reor
ient.nii.gz'),
    mask_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/s
ub-02/ses-01/workspace_24276/02-brainmask/sub-02_ses-01_run-24276_mod-FLAIR_brai
nmask.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_24276/03-biasfield'),
    entities={'sub': '02', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '24276'},
    quick=False,
)
[command] - N4BiasFieldCorrection -d 3 -i
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/01-reorient/sub-02_ses-01_run-24276_mod-FLAIR_reorient.nii.gz -s 1 -b
[1x1x1,3] -c [50x50x50x50,0.001] -t [0.15,0.01,200] -x
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/02-brainmask/sub-02_ses-01_run-24276_mod-FLAIR_brainmask.nii.gz -o
[/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_2
4276/03-biasfield/sub-02_ses-01_run-24276_mod-FLAIR_biascorrected.nii.gz,/tmp/br
ainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24276/03-
biasfield/sub-02_ses-01_run-24276_mod-FLAIR_biasfield.nii.gz] -v
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/03-biasfield/sub-02_ses-01_run-24276_mod-FLAIR_biascorrected.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/03-biasfield/sub-02_ses-01_run-24276_mod-FLAIR_biasfield.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applymask -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/03-biasfield/sub-02_ses-01_run-24276_mod-FLAIR_biascorrected.nii.gz
-mask-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/02-brainmask/sub-02_ses-01_run-24276_mod-FLAIR_brainmask.nii.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/03-biasfield -entities sub-02_modality-FLAIR_mod-FLAIR_ses-01_run-24276
-verbose True -dryrun True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.applymask(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_24276/03-biasfield/sub-02_ses-01_run-24276_mod-FLAIR_bia
scorrected.nii.gz'),
    mask_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/s
ub-02/ses-01/workspace_24276/02-brainmask/sub-02_ses-01_run-24276_mod-FLAIR_brai
nmask.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_24276/03-biasfield'),
    entities={'sub': '02', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '24276'},
)
[command] - fslmaths
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/03-biasfield/sub-02_ses-01_run-24276_mod-FLAIR_biascorrected.nii.gz -mas
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/02-brainmask/sub-02_ses-01_run-24276_mod-FLAIR_brainmask.nii.gz
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/03-biasfield/sub-02_ses-01_run-24276_mod-FLAIR_applymask.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/03-biasfield/sub-02_ses-01_run-24276_mod-FLAIR_applymask.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface scale -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/03-biasfield/sub-02_ses-01_run-24276_mod-FLAIR_applymask.nii.gz -scale 1
-output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/04-scale -entities sub-02_modality-FLAIR_mod-FLAIR_ses-01_run-24276
-interpolation spline -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.scale(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_24276/03-biasfield/sub-02_ses-01_run-24276_mod-FLAIR_app
lymask.nii.gz'),
    scale=1,
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_24276/04-scale'),
    entities={'sub': '02', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '24276'},
    interpolation='spline',
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/03-biasfield/sub-02_ses-01_run-24276_mod-FLAIR_applymask.nii.gz -ref
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/03-biasfield/sub-02_ses-01_run-24276_mod-FLAIR_applymask.nii.gz -applyisoxfm
1 -interp spline -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/04-scale/sub-02_ses-01_run-24276_mod-FLAIR_scale.nii.gz -omat
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/04-scale/sub-02_ses-01_run-24276_mod-FLAIR_scale.txt -verbose 1
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/04-scale/sub-02_ses-01_run-24276_mod-FLAIR_scale.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/04-scale/sub-02_ses-01_run-24276_mod-FLAIR_scale.txt
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface affine -anatomical-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/04-scale/sub-02_ses-01_run-24276_mod-FLAIR_scale.nii.gz -template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/05-affine -entities sub-02_modality-FLAIR_mod-FLAIR_ses-01_run-24276 -rigid
False -quick False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.affine(
    anatomical_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subj
ects/sub-02/ses-01/workspace_24276/04-scale/sub-02_ses-01_run-24276_mod-FLAIR_sc
ale.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T2_1mm_brain.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_24276/05-affine'),
    entities={'sub': '02', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '24276'},
    rigid=False,
    quick=False,
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/04-scale/sub-02_ses-01_run-24276_mod-FLAIR_scale.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -cost normmi -searchcost normmi -anglerep euler -bins 256 -interp trilinear
-dof 9 -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/05-affine/sub-02_ses-01_run-24276_mod-FLAIR_affine.nii.gz -omat
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/05-affine/sub-02_ses-01_run-24276_mod-FLAIR_affine.txt -verbose 1
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/05-affine/sub-02_ses-01_run-24276_mod-FLAIR_affine.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/05-affine/sub-02_ses-01_run-24276_mod-FLAIR_affine.txt
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applyaffine -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/03-biasfield/sub-02_ses-01_run-24276_mod-FLAIR_biascorrected.nii.gz
-template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -transform-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/05-affine/sub-02_ses-01_run-24276_mod-FLAIR_affine.txt -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/06-applyaffine -entities sub-02_modality-FLAIR_mod-FLAIR_ses-01_run-24276
-interpolation spline -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.applyaffine(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_24276/03-biasfield/sub-02_ses-01_run-24276_mod-FLAIR_bia
scorrected.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T2_1mm_brain.nii.gz'),
    transform_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subje
cts/sub-02/ses-01/workspace_24276/05-affine/sub-02_ses-01_run-24276_mod-FLAIR_af
fine.txt'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_24276/06-applyaffine'),
    entities={'sub': '02', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '24276'},
    interpolation='spline',
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/03-biasfield/sub-02_ses-01_run-24276_mod-FLAIR_biascorrected.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -init
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/05-affine/sub-02_ses-01_run-24276_mod-FLAIR_affine.txt -interp spline
-applyxfm -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/06-applyaffine/sub-02_ses-01_run-24276_mod-FLAIR_applyaffine.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/06-applyaffine/sub-02_ses-01_run-24276_mod-FLAIR_applyaffine.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applyaffine -image-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/02-brainmask/sub-02_ses-01_run-24276_mod-FLAIR_brainmask.nii.gz
-template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -transform-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/05-affine/sub-02_ses-01_run-24276_mod-FLAIR_affine.txt -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/07-applyaffine -entities sub-02_modality-FLAIR_mod-FLAIR_ses-01_run-24276
-interpolation nearestneighbour -verbose True -dryrun True -no-color False
-skip-run-check False -cat12-file /opt/cat12/standalone/cat_standalone.sh
-spm12-dir /opt/cat12 -matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.fsl.applyaffine(
    image_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_24276/02-brainmask/sub-02_ses-01_run-24276_mod-FLAIR_bra
inmask.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T2_1mm_brain.nii.gz'),
    transform_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subje
cts/sub-02/ses-01/workspace_24276/05-affine/sub-02_ses-01_run-24276_mod-FLAIR_af
fine.txt'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01/workspace_24276/07-applyaffine'),
    entities={'sub': '02', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '24276'},
    interpolation='nearestneighbour',
)
[command] - flirt -in
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/02-brainmask/sub-02_ses-01_run-24276_mod-FLAIR_brainmask.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T2_1mm_brain.ni
i.gz -init
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/05-affine/sub-02_ses-01_run-24276_mod-FLAIR_affine.txt -interp
nearestneighbour -applyxfm -out
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/07-applyaffine/sub-02_ses-01_run-24276_mod-FLAIR_applyaffine.nii.gz
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/07-applyaffine/sub-02_ses-01_run-24276_mod-FLAIR_applyaffine.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface copyfiles -source-files
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24
276/06-applyaffine/sub-02_ses-01_run-24276_mod-FLAIR_applyaffine.nii.gz,/tmp/bra
inprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24276/07-a
pplyaffine/sub-02_ses-01_run-24276_mod-FLAIR_applyaffine.nii.gz,/tmp/brainprep-q
uasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/workspace_24276/05-affine/su
b-02_ses-01_run-24276_mod-FLAIR_affine.txt -destination-files
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/sub-02_ses-0
1_run-24276_FLAIR.nii.gz,/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/s
ub-02/ses-01/sub-02_ses-01_run-24276_mod-FLAIR_brainmask.nii.gz,/tmp/brainprep-q
uasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/sub-02_ses-01_run-24276_mod-
FLAIR_affine.txt -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01 -move-files
False -dryrun False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.utils.copyfiles(
    source_files=[PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjec
ts/sub-02/ses-01/workspace_24276/06-applyaffine/sub-02_ses-01_run-24276_mod-FLAI
R_applyaffine.nii.gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/w
orkspace_24276/07-applyaffine/sub-02_ses-01_run-24276_mod-FLAIR_applyaffine.nii.
gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/w
orkspace_24276/05-affine/sub-02_ses-01_run-24276_mod-FLAIR_affine.txt')],
    destination_files=[PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/s
ubjects/sub-02/ses-01/sub-02_ses-01_run-24276_FLAIR.nii.gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/s
ub-02_ses-01_run-24276_mod-FLAIR_brainmask.nii.gz'),
PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-02/ses-01/s
ub-02_ses-01_run-24276_mod-FLAIR_affine.txt')],
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/
sub-02/ses-01'),
    move_files=False,
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[title] - Subject Level Quasi-RAW done.
__________________________________________________________________0.09s, 0.00min
[title] - Group Level Quasi-RAW...
________________________________________________________________________________
[call] brainprep.workflow.quasiraw.brainprep_group_quasiraw(
    modality='FLAIR',
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw'),
    correlation_threshold=0.5,
    keep_intermediate=False,
)
[info] - setting template file:
/home/runner/work/brainprep/brainprep/doc/../brainprep/resources/MNI152_T2_1mm_b
rain.nii.gz
[command] - brainprep interface mean-correlation -data-files-regex
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-*/ses-*/*_FLAIR.nii.gz
-atlas-file
/home/runner/work/brainprep/brainprep/doc/../brainprep/resources/MNI152_T2_1mm_b
rain.nii.gz -output-dir /tmp/brainprep-quasiraw/derivatives/quasiraw
-correlation-threshold 0.5 -suffix _FLAIR -dryrun False -verbose True -dryrun
True -no-color False -skip-run-check False -cat12-file
/opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12 -matlab-dir
/opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.qualcheck.mean_correlation(
    data_files_regex=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/sub
jects/sub-*/ses-*/*_FLAIR.nii.gz'),
    atlas_file=PosixPath('/home/runner/work/brainprep/brainprep/doc/../brainprep
/resources/MNI152_T2_1mm_brain.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_c
heck'),
    correlation_threshold=0.5,
    suffix='_FLAIR',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_check/mean_correlations_FLA
IR.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-histogram -table-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_check/mean_correlations_FLA
IR.tsv -col-name mean_correlation -output-dir
/tmp/brainprep-quasiraw/derivatives/quasiraw -bar-coords 0.5 -suffix _FLAIR
-dryrun False -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.plotting.plot_histogram(
    table_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_c
heck/mean_correlations_FLAIR.tsv'),
    col_name='mean_correlation',
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/figures')
,
    bar_coords=[0.5],
    suffix='_FLAIR',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/figures/histogram_mean_correlation_
FLAIR.png
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface incremental-pca -image-files-regex
/tmp/brainprep-quasiraw/derivatives/quasiraw/subjects/sub-*/ses-*/*_FLAIR.nii.gz
-output-dir /tmp/brainprep-quasiraw/derivatives/quasiraw -batch-size 50 -suffix
_FLAIR -dryrun False -verbose True -dryrun True -no-color False -skip-run-check
False -cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.qualcheck.incremental_pca(
    image_files_regex=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/su
bjects/sub-*/ses-*/*_FLAIR.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_c
heck'),
    batch_size=50,
    suffix='_FLAIR',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_check/pca_FLAIR.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-pca -pca-file
/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_check/pca_FLAIR.tsv
-output-dir /tmp/brainprep-quasiraw/derivatives/quasiraw -suffix _FLAIR -dryrun
False -verbose True -dryrun True -no-color False -skip-run-check False
-cat12-file /opt/cat12/standalone/cat_standalone.sh -spm12-dir /opt/cat12
-matlab-dir /opt/MCR-2017b/v93 -tpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/tpm/TPM.nii -darteltpm-file
/opt/cat12/spm12_mcr/home/gaser/gaser/spm/spm12/toolbox/cat12/templates_MNI152NL
in2009cAsym/Template_1_Dartel.nii -mni-2iso-file
/opt/fsl/data/standard/MNI152_T1_2mm.nii.gz -geolab-atlas-dir /opt/geolab/atlas
________________________________________________________________________________
[call] brainprep.interfaces.plotting.plot_pca(
    pca_file=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/quality_che
ck/pca_FLAIR.tsv'),
    output_dir=PosixPath('/tmp/brainprep-quasiraw/derivatives/quasiraw/figures')
,
    suffix='_FLAIR',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-quasiraw/derivatives/quasiraw/figures/pca_FLAIR.png
__________________________________________________________________0.00s, 0.00min
[title] - Group Level Quasi-RAW done.
__________________________________________________________________0.04s, 0.00min

CLI

Let’s now generate the same analysis using the CLI. The goal here is to translate the workflow calls into explicit shell commands. See user guide for details.

from pprint import pprint

commands = []
commands.append(
    [
        [
            "brainprep", "subject-level-quasiraw",
            "--anatomical_file", str(subject_data.anat),
            "--output-dir", str(outdir),
            "--keep-intermediate",
        ]
        for modality_data in data.values()
        for subject_data in modality_data.values()
    ]
)
commands.append(
    [
        [
            "brainprep", "group-level-quasiraw",
            "--modality", modality,
            "--output-dir", str(outdir),
        ]
        for modality in data.keys()
    ]
)
pprint(commands)

[[['brainprep',
   'subject-level-quasiraw',
   '--anatomical_file',
   '/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-quasiraw',
   '--keep-intermediate'],
  ['brainprep',
   'subject-level-quasiraw',
   '--anatomical_file',
   '/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-quasiraw',
   '--keep-intermediate'],
  ['brainprep',
   'subject-level-quasiraw',
   '--anatomical_file',
   '/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_T2w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-quasiraw',
   '--keep-intermediate'],
  ['brainprep',
   'subject-level-quasiraw',
   '--anatomical_file',
   '/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_T2w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-quasiraw',
   '--keep-intermediate'],
  ['brainprep',
   'subject-level-quasiraw',
   '--anatomical_file',
   '/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_FLAIR.nii.gz',
   '--output-dir',
   '/tmp/brainprep-quasiraw',
   '--keep-intermediate'],
  ['brainprep',
   'subject-level-quasiraw',
   '--anatomical_file',
   '/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_FLAIR.nii.gz',
   '--output-dir',
   '/tmp/brainprep-quasiraw',
   '--keep-intermediate']],
 [['brainprep',
   'group-level-quasiraw',
   '--modality',
   'T1w',
   '--output-dir',
   '/tmp/brainprep-quasiraw'],
  ['brainprep',
   'group-level-quasiraw',
   '--modality',
   'T2w',
   '--output-dir',
   '/tmp/brainprep-quasiraw'],
  ['brainprep',
   'group-level-quasiraw',
   '--modality',
   'FLAIR',
   '--output-dir',
   '/tmp/brainprep-quasiraw']]]

Container

Note that the commands generated by the CLI are not limited to being displayed for reference; they can also be executed directly within the workflow‑dedicated container. By running the commands inside the container, you benefit from a controlled runtime context where all necessary dependencies, libraries, and configuration files are already available. In practice, this means that once the CLI has produced the appropriate instructions, you can simply copy and run them inside the container to achieve the intended results. You can find the BrainPrep images on Docker Hub: Neurospin Docker Hub.

Estimated memory usage: 111 MB