Defacing

Simple example.

Example on how to run the defacing 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)

[info] - downloading:
https://raw.githubusercontent.com/muschellij2/open_ms_data/refs/heads/master/cro
ss_sectional/raw/patient01/T1W.nii.gz
[info] - downloading:
https://raw.githubusercontent.com/muschellij2/open_ms_data/refs/heads/master/cro
ss_sectional/raw/patient02/T1W.nii.gz
[info] - downloading:
https://raw.githubusercontent.com/muschellij2/open_ms_data/refs/heads/master/cro
ss_sectional/raw/patient01/T2W.nii.gz
[info] - downloading:
https://raw.githubusercontent.com/muschellij2/open_ms_data/refs/heads/master/cro
ss_sectional/raw/patient02/T2W.nii.gz
[info] - downloading:
https://raw.githubusercontent.com/muschellij2/open_ms_data/refs/heads/master/cro
ss_sectional/raw/patient01/FLAIR.nii.gz
[info] - downloading:
https://raw.githubusercontent.com/muschellij2/open_ms_data/refs/heads/master/cro
ss_sectional/raw/patient02/FLAIR.nii.gz
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 preprocessing using the 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_defacing,
    brainprep_group_defacing,
)
from brainprep.config import Config

outdir = Path("/tmp/brainprep-defacing")
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_defacing(
                anatomical_file=subject_data.anat,
                output_dir=outdir,
                keep_intermediate=True,
            )
            outputs.deface_anatomical_file.touch(exist_ok=True)
            outputs.mask_file.touch(exist_ok=True)
        outputs = brainprep_group_defacing(
            modality=modality,
            output_dir=outdir,
        )

[warn] - BIDS file name does not contain run key: sub-01_T1w.nii.gz
[title] - Subject Level Defacing...
________________________________________________________________________________
[call] brainprep.workflow.defacing.brainprep_defacing(
    anatomical_file=PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/su
b-01_T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01'),
    keep_intermediate=True,
    kwargs={'entities': {'sub': '01', 'modality': 'T1w', 'mod': 'T1w', 'ses':
'01', 'run': '34706'}},
)
[info] - setting workspace directory:
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/01-reorient/sub-01_ses-01_run-34706_mod-T1w_reorient.nii.gz -o
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/02-brainmask/sub-01_ses-01_run-34706_mod-T1w_brain.nii.gz -m
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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 deface -t1-file
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/03-deface -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.deface(
    t1_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub
-01/ses-01/workspace_34706/01-reorient/sub-01_ses-01_run-34706_mod-T1w_reorient.
nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/workspace_34706/03-deface'),
    entities={'sub': '01', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'34706'},
)
[command] - fsl_deface
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/01-reorient/sub-01_ses-01_run-34706_mod-T1w_reorient.nii.gz
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/03-deface/sub-01_ses-01_run-34706_mod-T1w_deface.nii.gz -d
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/03-deface/sub-01_ses-01_run-34706_mod-T1w_defacemask.nii.gz -m13
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/03-deface/sub-01_ses-01_run-34706_mod-T1w_defaceaffine.mat -f 0.5 -B
[command] - convert_xfm -omat
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/03-deface/sub-01_ses-01_run-34706_mod-T1w_defaceaffine.mat -concat
/home/runner/work/brainprep/brainprep/doc/../brainprep/resources/MNI_BigFov_to_M
NI.mat
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/03-deface/sub-01_ses-01_run-34706_mod-T1w_defaceaffine.mat
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/03-deface/sub-01_ses-01_run-34706_mod-T1w_deface.nii.gz
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/03-deface/sub-01_ses-01_run-34706_mod-T1w_defacemask.nii.gz
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/03-deface/sub-01_ses-01_run-34706_mod-T1w_defaceaffine.mat
__________________________________________________________________0.01s, 0.00min
[command] - brainprep interface applyaffine -image-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/01-reorient/sub-01_ses-01_run-34706_mod-T1w_reorient.nii.gz -template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T1_1mm_brain.ni
i.gz -transform-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/03-deface/sub-01_ses-01_run-34706_mod-T1w_defaceaffine.mat -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/03-deface -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-defacing/derivatives/defacing/subjects/
sub-01/ses-01/workspace_34706/01-reorient/sub-01_ses-01_run-34706_mod-T1w_reorie
nt.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T1_1mm_brain.nii.gz'),
    transform_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subje
cts/sub-01/ses-01/workspace_34706/03-deface/sub-01_ses-01_run-34706_mod-T1w_defa
ceaffine.mat'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/workspace_34706/03-deface'),
    entities={'sub': '01', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'34706'},
    interpolation='spline',
)
[command] - flirt -in
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/01-reorient/sub-01_ses-01_run-34706_mod-T1w_reorient.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T1_1mm_brain.ni
i.gz -init
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/03-deface/sub-01_ses-01_run-34706_mod-T1w_defaceaffine.mat -interp spline
-applyxfm -out
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/03-deface/sub-01_ses-01_run-34706_mod-T1w_applyaffine.nii.gz
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/03-deface/sub-01_ses-01_run-34706_mod-T1w_applyaffine.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface maskdiff -mask1-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/02-brainmask/sub-01_ses-01_run-34706_mod-T1w_brainmask.nii.gz -mask2-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/03-deface/sub-01_ses-01_run-34706_mod-T1w_defacemask.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/quality_chec
k -entities sub-01_modality-T1w_mod-T1w_ses-01_run-34706 -inv-mask1 False
-inv-mask2 True -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.maskdiff(
    mask1_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/workspace_34706/02-brainmask/sub-01_ses-01_run-34706_mod-T1w_brain
mask.nii.gz'),
    mask2_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/workspace_34706/03-deface/sub-01_ses-01_run-34706_mod-T1w_defacema
sk.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/quality_check'),
    entities={'sub': '01', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'34706'},
    inv_mask1=False,
    inv_mask2=True,
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/quality_chec
k/sub-01_ses-01_run-34706_mod-T1w_maskdiff.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mean-correlation -data-files-regex
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/03-deface/sub-01_ses-01_run-34706_mod-T1w_applyaffine.nii.gz -atlas-file
/home/runner/work/brainprep/brainprep/doc/../brainprep/resources/MNI152_T1_1mm_b
rain.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01
-correlation-threshold None -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-defacing/derivatives/defacing/sub
jects/sub-01/ses-01/workspace_34706/03-deface/sub-01_ses-01_run-34706_mod-T1w_ap
plyaffine.nii.gz'),
    atlas_file=PosixPath('/home/runner/work/brainprep/brainprep/doc/../brainprep
/resources/MNI152_T1_1mm_brain.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/quality_check'),
    correlation_threshold=None,
    suffix='_T1w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/quality_chec
k/mean_correlations_T1w.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-defacing-mosaic -im-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/03-deface/sub-01_ses-01_run-34706_mod-T1w_defacemask.nii.gz -mask-file
/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_T1w.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01 -entities
sub-01_modality-T1w_mod-T1w_ses-01_run-34706 -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_defacing_mosaic(
    im_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub
-01/ses-01/workspace_34706/03-deface/sub-01_ses-01_run-34706_mod-T1w_defacemask.
nii.gz'),
    mask_file=PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_T
1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/figures'),
    entities={'sub': '01', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'34706'},
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/figures/sub-
01_ses-01_run-34706_mod-T1w_defacemosaic.png
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface copyfiles -source-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34
706/03-deface/sub-01_ses-01_run-34706_mod-T1w_deface.nii.gz,/tmp/brainprep-defac
ing/derivatives/defacing/subjects/sub-01/ses-01/workspace_34706/03-deface/sub-01
_ses-01_run-34706_mod-T1w_defacemask.nii.gz,/tmp/brainprep-defacing/derivatives/
defacing/subjects/sub-01/ses-01/workspace_34706/03-deface/sub-01_ses-01_run-3470
6_mod-T1w_defaceaffine.mat,/tmp/brainprep-defacing/derivatives/defacing/subjects
/sub-01/ses-01/quality_check/mean_correlations_T1w.tsv -destination-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/sub-01_ses-0
1_run-34706_T1w.nii.gz,/tmp/brainprep-defacing/derivatives/defacing/subjects/sub
-01/ses-01/sub-01_ses-01_run-34706_mod-T1w_defacemask.nii.gz,/tmp/brainprep-defa
cing/derivatives/defacing/subjects/sub-01/ses-01/sub-01_ses-01_run-34706_mod-T1w
_affine.txt,/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/
quality_check/sub-01_ses-01_run-34706_mod-T1w_corr.tsv -output-dir
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjec
ts/sub-01/ses-01/workspace_34706/03-deface/sub-01_ses-01_run-34706_mod-T1w_defac
e.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/w
orkspace_34706/03-deface/sub-01_ses-01_run-34706_mod-T1w_defacemask.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/w
orkspace_34706/03-deface/sub-01_ses-01_run-34706_mod-T1w_defaceaffine.mat'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/q
uality_check/mean_correlations_T1w.tsv')],
    destination_files=[PosixPath('/tmp/brainprep-defacing/derivatives/defacing/s
ubjects/sub-01/ses-01/sub-01_ses-01_run-34706_T1w.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/s
ub-01_ses-01_run-34706_mod-T1w_defacemask.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/s
ub-01_ses-01_run-34706_mod-T1w_affine.txt'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/q
uality_check/sub-01_ses-01_run-34706_mod-T1w_corr.tsv')],
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01'),
    move_files=False,
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface copyfiles -source-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/quality_chec
k/mean_correlations_T1w.tsv -destination-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/quality_chec
k/sub-01_ses-01_run-34706_mod-T1w_corr.tsv -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01 -move-files
True -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-defacing/derivatives/defacing/subjec
ts/sub-01/ses-01/quality_check/mean_correlations_T1w.tsv')],
    destination_files=[PosixPath('/tmp/brainprep-defacing/derivatives/defacing/s
ubjects/sub-01/ses-01/quality_check/sub-01_ses-01_run-34706_mod-T1w_corr.tsv')],
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01'),
    move_files=True,
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[title] - Subject Level Defacing done.
__________________________________________________________________0.09s, 0.00min
[warn] - BIDS file name does not contain run key: sub-02_T1w.nii.gz
[title] - Subject Level Defacing...
________________________________________________________________________________
[call] brainprep.workflow.defacing.brainprep_defacing(
    anatomical_file=PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/su
b-02_T1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01'),
    keep_intermediate=True,
    kwargs={'entities': {'sub': '02', 'modality': 'T1w', 'mod': 'T1w', 'ses':
'01', 'run': '21669'}},
)
[info] - setting workspace directory:
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/01-reorient/sub-02_ses-01_run-21669_mod-T1w_reorient.nii.gz -o
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/02-brainmask/sub-02_ses-01_run-21669_mod-T1w_brain.nii.gz -m
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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 deface -t1-file
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/03-deface -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.deface(
    t1_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub
-02/ses-01/workspace_21669/01-reorient/sub-02_ses-01_run-21669_mod-T1w_reorient.
nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/workspace_21669/03-deface'),
    entities={'sub': '02', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'21669'},
)
[command] - fsl_deface
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/01-reorient/sub-02_ses-01_run-21669_mod-T1w_reorient.nii.gz
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/03-deface/sub-02_ses-01_run-21669_mod-T1w_deface.nii.gz -d
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/03-deface/sub-02_ses-01_run-21669_mod-T1w_defacemask.nii.gz -m13
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/03-deface/sub-02_ses-01_run-21669_mod-T1w_defaceaffine.mat -f 0.5 -B
[command] - convert_xfm -omat
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/03-deface/sub-02_ses-01_run-21669_mod-T1w_defaceaffine.mat -concat
/home/runner/work/brainprep/brainprep/doc/../brainprep/resources/MNI_BigFov_to_M
NI.mat
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/03-deface/sub-02_ses-01_run-21669_mod-T1w_defaceaffine.mat
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/03-deface/sub-02_ses-01_run-21669_mod-T1w_deface.nii.gz
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/03-deface/sub-02_ses-01_run-21669_mod-T1w_defacemask.nii.gz
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/03-deface/sub-02_ses-01_run-21669_mod-T1w_defaceaffine.mat
__________________________________________________________________0.01s, 0.00min
[command] - brainprep interface applyaffine -image-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/01-reorient/sub-02_ses-01_run-21669_mod-T1w_reorient.nii.gz -template-file
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T1_1mm_brain.ni
i.gz -transform-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/03-deface/sub-02_ses-01_run-21669_mod-T1w_defaceaffine.mat -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/03-deface -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-defacing/derivatives/defacing/subjects/
sub-02/ses-01/workspace_21669/01-reorient/sub-02_ses-01_run-21669_mod-T1w_reorie
nt.nii.gz'),
    template_file=PosixPath('/home/runner/work/brainprep/brainprep/brainprep/res
ources/MNI152_T1_1mm_brain.nii.gz'),
    transform_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subje
cts/sub-02/ses-01/workspace_21669/03-deface/sub-02_ses-01_run-21669_mod-T1w_defa
ceaffine.mat'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/workspace_21669/03-deface'),
    entities={'sub': '02', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'21669'},
    interpolation='spline',
)
[command] - flirt -in
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/01-reorient/sub-02_ses-01_run-21669_mod-T1w_reorient.nii.gz -ref
/home/runner/work/brainprep/brainprep/brainprep/resources/MNI152_T1_1mm_brain.ni
i.gz -init
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/03-deface/sub-02_ses-01_run-21669_mod-T1w_defaceaffine.mat -interp spline
-applyxfm -out
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/03-deface/sub-02_ses-01_run-21669_mod-T1w_applyaffine.nii.gz
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/03-deface/sub-02_ses-01_run-21669_mod-T1w_applyaffine.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface maskdiff -mask1-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/02-brainmask/sub-02_ses-01_run-21669_mod-T1w_brainmask.nii.gz -mask2-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/03-deface/sub-02_ses-01_run-21669_mod-T1w_defacemask.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/quality_chec
k -entities sub-02_modality-T1w_mod-T1w_ses-01_run-21669 -inv-mask1 False
-inv-mask2 True -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.maskdiff(
    mask1_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/workspace_21669/02-brainmask/sub-02_ses-01_run-21669_mod-T1w_brain
mask.nii.gz'),
    mask2_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/workspace_21669/03-deface/sub-02_ses-01_run-21669_mod-T1w_defacema
sk.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/quality_check'),
    entities={'sub': '02', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'21669'},
    inv_mask1=False,
    inv_mask2=True,
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/quality_chec
k/sub-02_ses-01_run-21669_mod-T1w_maskdiff.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mean-correlation -data-files-regex
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/03-deface/sub-02_ses-01_run-21669_mod-T1w_applyaffine.nii.gz -atlas-file
/home/runner/work/brainprep/brainprep/doc/../brainprep/resources/MNI152_T1_1mm_b
rain.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01
-correlation-threshold None -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-defacing/derivatives/defacing/sub
jects/sub-02/ses-01/workspace_21669/03-deface/sub-02_ses-01_run-21669_mod-T1w_ap
plyaffine.nii.gz'),
    atlas_file=PosixPath('/home/runner/work/brainprep/brainprep/doc/../brainprep
/resources/MNI152_T1_1mm_brain.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/quality_check'),
    correlation_threshold=None,
    suffix='_T1w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/quality_chec
k/mean_correlations_T1w.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-defacing-mosaic -im-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/03-deface/sub-02_ses-01_run-21669_mod-T1w_defacemask.nii.gz -mask-file
/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_T1w.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01 -entities
sub-02_modality-T1w_mod-T1w_ses-01_run-21669 -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_defacing_mosaic(
    im_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub
-02/ses-01/workspace_21669/03-deface/sub-02_ses-01_run-21669_mod-T1w_defacemask.
nii.gz'),
    mask_file=PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_T
1w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/figures'),
    entities={'sub': '02', 'modality': 'T1w', 'mod': 'T1w', 'ses': '01', 'run':
'21669'},
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/figures/sub-
02_ses-01_run-21669_mod-T1w_defacemosaic.png
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface copyfiles -source-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21
669/03-deface/sub-02_ses-01_run-21669_mod-T1w_deface.nii.gz,/tmp/brainprep-defac
ing/derivatives/defacing/subjects/sub-02/ses-01/workspace_21669/03-deface/sub-02
_ses-01_run-21669_mod-T1w_defacemask.nii.gz,/tmp/brainprep-defacing/derivatives/
defacing/subjects/sub-02/ses-01/workspace_21669/03-deface/sub-02_ses-01_run-2166
9_mod-T1w_defaceaffine.mat,/tmp/brainprep-defacing/derivatives/defacing/subjects
/sub-02/ses-01/quality_check/mean_correlations_T1w.tsv -destination-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/sub-02_ses-0
1_run-21669_T1w.nii.gz,/tmp/brainprep-defacing/derivatives/defacing/subjects/sub
-02/ses-01/sub-02_ses-01_run-21669_mod-T1w_defacemask.nii.gz,/tmp/brainprep-defa
cing/derivatives/defacing/subjects/sub-02/ses-01/sub-02_ses-01_run-21669_mod-T1w
_affine.txt,/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/
quality_check/sub-02_ses-01_run-21669_mod-T1w_corr.tsv -output-dir
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjec
ts/sub-02/ses-01/workspace_21669/03-deface/sub-02_ses-01_run-21669_mod-T1w_defac
e.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/w
orkspace_21669/03-deface/sub-02_ses-01_run-21669_mod-T1w_defacemask.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/w
orkspace_21669/03-deface/sub-02_ses-01_run-21669_mod-T1w_defaceaffine.mat'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/q
uality_check/mean_correlations_T1w.tsv')],
    destination_files=[PosixPath('/tmp/brainprep-defacing/derivatives/defacing/s
ubjects/sub-02/ses-01/sub-02_ses-01_run-21669_T1w.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/s
ub-02_ses-01_run-21669_mod-T1w_defacemask.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/s
ub-02_ses-01_run-21669_mod-T1w_affine.txt'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/q
uality_check/sub-02_ses-01_run-21669_mod-T1w_corr.tsv')],
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01'),
    move_files=False,
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface copyfiles -source-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/quality_chec
k/mean_correlations_T1w.tsv -destination-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/quality_chec
k/sub-02_ses-01_run-21669_mod-T1w_corr.tsv -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01 -move-files
True -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-defacing/derivatives/defacing/subjec
ts/sub-02/ses-01/quality_check/mean_correlations_T1w.tsv')],
    destination_files=[PosixPath('/tmp/brainprep-defacing/derivatives/defacing/s
ubjects/sub-02/ses-01/quality_check/sub-02_ses-01_run-21669_mod-T1w_corr.tsv')],
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01'),
    move_files=True,
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[title] - Subject Level Defacing done.
__________________________________________________________________0.08s, 0.00min
[title] - Group Level Defacing...
________________________________________________________________________________
[call] brainprep.workflow.defacing.brainprep_group_defacing(
    modality='T1w',
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing'),
    overlap_threshold=0.05,
    correlation_threshold=0.5,
    keep_intermediate=False,
)
[command] - brainprep interface mean-correlation -data-files-regex
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-*/ses-*/quality_check/
*mod-T1w_corr.tsv -atlas-file None -output-dir
/tmp/brainprep-defacing/derivatives/defacing -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-defacing/derivatives/defacing/sub
jects/sub-*/ses-*/quality_check/*mod-T1w_corr.tsv'),
    atlas_file=None,
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/quality_c
heck'),
    correlation_threshold=0.5,
    suffix='_T1w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/quality_check/mean_correlations_T1w
.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-histogram -table-file
/tmp/brainprep-defacing/derivatives/defacing/quality_check/mean_correlations_T1w
.tsv -col-name mean_correlation -output-dir
/tmp/brainprep-defacing/derivatives/defacing -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-defacing/derivatives/defacing/quality_c
heck/mean_correlations_T1w.tsv'),
    col_name='mean_correlation',
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/figures')
,
    bar_coords=[0.5],
    suffix='_T1w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/figures/histogram_mean_correlation_
T1w.png
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mask-overlap -maskdiff-files-regex
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-*/ses-*/quality_check/
*mod-T1w_maskdiff.tsv -output-dir /tmp/brainprep-defacing/derivatives/defacing
-overlap-threshold 0.05 -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.mask_overlap(
    maskdiff_files_regex=PosixPath('/tmp/brainprep-defacing/derivatives/defacing
/subjects/sub-*/ses-*/quality_check/*mod-T1w_maskdiff.tsv'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/quality_c
heck'),
    overlap_threshold=0.05,
    suffix='_T1w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/quality_check/mask_overlap_T1w.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-histogram -table-file
/tmp/brainprep-defacing/derivatives/defacing/quality_check/mask_overlap_T1w.tsv
-col-name overlap -output-dir /tmp/brainprep-defacing/derivatives/defacing
-bar-coords 0.05 -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-defacing/derivatives/defacing/quality_c
heck/mask_overlap_T1w.tsv'),
    col_name='overlap',
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/figures')
,
    bar_coords=[0.05],
    suffix='_T1w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/figures/histogram_overlap_T1w.png
__________________________________________________________________0.00s, 0.00min
[title] - Group Level Defacing done.
__________________________________________________________________0.03s, 0.00min
[warn] - BIDS file name does not contain run key: sub-01_T2w.nii.gz
[title] - Subject Level Defacing...
________________________________________________________________________________
[call] brainprep.workflow.defacing.brainprep_defacing(
    anatomical_file=PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/su
b-01_T2w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01'),
    keep_intermediate=True,
    kwargs={'entities': {'sub': '01', 'modality': 'T2w', 'mod': 'T2w', 'ses':
'01', 'run': '17909'}},
)
[info] - setting workspace directory:
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/01-reorient/sub-01_ses-01_run-17909_mod-T2w_reorient.nii.gz -o
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/02-brainmask/sub-01_ses-01_run-17909_mod-T2w_brain.nii.gz -m
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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
[info] - using T1w:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/sub-01_ses-0
1_run-34706_T1w.nii.gz
[info] - using defacing mask:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/sub-01_ses-0
1_run-34706_mod-T1w_defacemask.nii.gz
[command] - brainprep interface affine -anatomical-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/sub-01_ses-0
1_run-34706_T1w.nii.gz -template-file
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface -entities sub-01_modality-T2w_mod-T2w_ses-01_run-17909 -rigid True
-quick True -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-defacing/derivatives/defacing/subj
ects/sub-01/ses-01/sub-01_ses-01_run-34706_T1w.nii.gz'),
    template_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjec
ts/sub-01/ses-01/workspace_17909/01-reorient/sub-01_ses-01_run-17909_mod-T2w_reo
rient.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/workspace_17909/03-deface'),
    entities={'sub': '01', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'17909'},
    rigid=True,
    quick=True,
)
[command] - flirt -in
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/sub-01_ses-0
1_run-34706_T1w.nii.gz -ref
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/01-reorient/sub-01_ses-01_run-17909_mod-T2w_reorient.nii.gz -cost normmi
-searchcost normmi -anglerep euler -bins 256 -interp trilinear -dof 6 -out
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface/sub-01_ses-01_run-17909_mod-T2w_affine.nii.gz -omat
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface/sub-01_ses-01_run-17909_mod-T2w_affine.txt -verbose 1 -searchrx
-30 30 -searchry -30 30 -searchrz -30 30
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface/sub-01_ses-01_run-17909_mod-T2w_affine.nii.gz
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface/sub-01_ses-01_run-17909_mod-T2w_affine.txt
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applyaffine -image-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/sub-01_ses-0
1_run-34706_mod-T1w_defacemask.nii.gz -template-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/01-reorient/sub-01_ses-01_run-17909_mod-T2w_reorient.nii.gz -transform-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface/sub-01_ses-01_run-17909_mod-T2w_affine.txt -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface -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-defacing/derivatives/defacing/subjects/
sub-01/ses-01/sub-01_ses-01_run-34706_mod-T1w_defacemask.nii.gz'),
    template_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjec
ts/sub-01/ses-01/workspace_17909/01-reorient/sub-01_ses-01_run-17909_mod-T2w_reo
rient.nii.gz'),
    transform_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subje
cts/sub-01/ses-01/workspace_17909/03-deface/sub-01_ses-01_run-17909_mod-T2w_affi
ne.txt'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/workspace_17909/03-deface'),
    entities={'sub': '01', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'17909'},
    interpolation='nearestneighbour',
)
[command] - flirt -in
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/sub-01_ses-0
1_run-34706_mod-T1w_defacemask.nii.gz -ref
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/01-reorient/sub-01_ses-01_run-17909_mod-T2w_reorient.nii.gz -init
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface/sub-01_ses-01_run-17909_mod-T2w_affine.txt -interp
nearestneighbour -applyxfm -out
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface/sub-01_ses-01_run-17909_mod-T2w_applyaffine.nii.gz
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface/sub-01_ses-01_run-17909_mod-T2w_applyaffine.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applymask -image-file
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface/sub-01_ses-01_run-17909_mod-T2w_applyaffine.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface -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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/s
ub-01/ses-01/workspace_17909/03-deface/sub-01_ses-01_run-17909_mod-T2w_applyaffi
ne.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/workspace_17909/03-deface'),
    entities={'sub': '01', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'17909'},
)
[command] - fslmaths
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/01-reorient/sub-01_ses-01_run-17909_mod-T2w_reorient.nii.gz -mas
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface/sub-01_ses-01_run-17909_mod-T2w_applyaffine.nii.gz
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface/sub-01_ses-01_run-17909_mod-T2w_applymask.nii.gz
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface/sub-01_ses-01_run-17909_mod-T2w_applymask.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface maskdiff -mask1-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/02-brainmask/sub-01_ses-01_run-17909_mod-T2w_brainmask.nii.gz -mask2-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface/sub-01_ses-01_run-17909_mod-T2w_applyaffine.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/quality_chec
k -entities sub-01_modality-T2w_mod-T2w_ses-01_run-17909 -inv-mask1 False
-inv-mask2 True -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.maskdiff(
    mask1_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/workspace_17909/02-brainmask/sub-01_ses-01_run-17909_mod-T2w_brain
mask.nii.gz'),
    mask2_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/workspace_17909/03-deface/sub-01_ses-01_run-17909_mod-T2w_applyaff
ine.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/quality_check'),
    entities={'sub': '01', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'17909'},
    inv_mask1=False,
    inv_mask2=True,
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/quality_chec
k/sub-01_ses-01_run-17909_mod-T2w_maskdiff.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mean-correlation -data-files-regex
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/01-reorient/sub-01_ses-01_run-17909_mod-T2w_reorient.nii.gz -atlas-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface/sub-01_ses-01_run-17909_mod-T2w_affine.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01
-correlation-threshold None -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-defacing/derivatives/defacing/sub
jects/sub-01/ses-01/workspace_17909/01-reorient/sub-01_ses-01_run-17909_mod-T2w_
reorient.nii.gz'),
    atlas_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/workspace_17909/03-deface/sub-01_ses-01_run-17909_mod-T2w_affine.n
ii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/quality_check'),
    correlation_threshold=None,
    suffix='_T2w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/quality_chec
k/mean_correlations_T2w.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-defacing-mosaic -im-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface/sub-01_ses-01_run-17909_mod-T2w_applyaffine.nii.gz -mask-file
/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_T2w.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01 -entities
sub-01_modality-T2w_mod-T2w_ses-01_run-17909 -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_defacing_mosaic(
    im_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub
-01/ses-01/workspace_17909/03-deface/sub-01_ses-01_run-17909_mod-T2w_applyaffine
.nii.gz'),
    mask_file=PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_T
2w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/figures'),
    entities={'sub': '01', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'17909'},
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/figures/sub-
01_ses-01_run-17909_mod-T2w_defacemosaic.png
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface copyfiles -source-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17
909/03-deface/sub-01_ses-01_run-17909_mod-T2w_applymask.nii.gz,/tmp/brainprep-de
facing/derivatives/defacing/subjects/sub-01/ses-01/workspace_17909/03-deface/sub
-01_ses-01_run-17909_mod-T2w_applyaffine.nii.gz,/tmp/brainprep-defacing/derivati
ves/defacing/subjects/sub-01/ses-01/workspace_17909/03-deface/sub-01_ses-01_run-
17909_mod-T2w_affine.txt,/tmp/brainprep-defacing/derivatives/defacing/subjects/s
ub-01/ses-01/quality_check/mean_correlations_T2w.tsv -destination-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/sub-01_ses-0
1_run-17909_T2w.nii.gz,/tmp/brainprep-defacing/derivatives/defacing/subjects/sub
-01/ses-01/sub-01_ses-01_run-17909_mod-T2w_defacemask.nii.gz,/tmp/brainprep-defa
cing/derivatives/defacing/subjects/sub-01/ses-01/sub-01_ses-01_run-17909_mod-T2w
_affine.txt,/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/
quality_check/sub-01_ses-01_run-17909_mod-T2w_corr.tsv -output-dir
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjec
ts/sub-01/ses-01/workspace_17909/03-deface/sub-01_ses-01_run-17909_mod-T2w_apply
mask.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/w
orkspace_17909/03-deface/sub-01_ses-01_run-17909_mod-T2w_applyaffine.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/w
orkspace_17909/03-deface/sub-01_ses-01_run-17909_mod-T2w_affine.txt'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/q
uality_check/mean_correlations_T2w.tsv')],
    destination_files=[PosixPath('/tmp/brainprep-defacing/derivatives/defacing/s
ubjects/sub-01/ses-01/sub-01_ses-01_run-17909_T2w.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/s
ub-01_ses-01_run-17909_mod-T2w_defacemask.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/s
ub-01_ses-01_run-17909_mod-T2w_affine.txt'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/q
uality_check/sub-01_ses-01_run-17909_mod-T2w_corr.tsv')],
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01'),
    move_files=False,
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface copyfiles -source-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/quality_chec
k/mean_correlations_T2w.tsv -destination-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/quality_chec
k/sub-01_ses-01_run-17909_mod-T2w_corr.tsv -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01 -move-files
True -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-defacing/derivatives/defacing/subjec
ts/sub-01/ses-01/quality_check/mean_correlations_T2w.tsv')],
    destination_files=[PosixPath('/tmp/brainprep-defacing/derivatives/defacing/s
ubjects/sub-01/ses-01/quality_check/sub-01_ses-01_run-17909_mod-T2w_corr.tsv')],
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01'),
    move_files=True,
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[title] - Subject Level Defacing done.
__________________________________________________________________0.09s, 0.00min
[warn] - BIDS file name does not contain run key: sub-02_T2w.nii.gz
[title] - Subject Level Defacing...
________________________________________________________________________________
[call] brainprep.workflow.defacing.brainprep_defacing(
    anatomical_file=PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/su
b-02_T2w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01'),
    keep_intermediate=True,
    kwargs={'entities': {'sub': '02', 'modality': 'T2w', 'mod': 'T2w', 'ses':
'01', 'run': '32679'}},
)
[info] - setting workspace directory:
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/01-reorient/sub-02_ses-01_run-32679_mod-T2w_reorient.nii.gz -o
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/02-brainmask/sub-02_ses-01_run-32679_mod-T2w_brain.nii.gz -m
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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
[info] - using T1w:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/sub-02_ses-0
1_run-21669_T1w.nii.gz
[info] - using defacing mask:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/sub-02_ses-0
1_run-21669_mod-T1w_defacemask.nii.gz
[command] - brainprep interface affine -anatomical-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/sub-02_ses-0
1_run-21669_T1w.nii.gz -template-file
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface -entities sub-02_modality-T2w_mod-T2w_ses-01_run-32679 -rigid True
-quick True -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-defacing/derivatives/defacing/subj
ects/sub-02/ses-01/sub-02_ses-01_run-21669_T1w.nii.gz'),
    template_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjec
ts/sub-02/ses-01/workspace_32679/01-reorient/sub-02_ses-01_run-32679_mod-T2w_reo
rient.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/workspace_32679/03-deface'),
    entities={'sub': '02', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'32679'},
    rigid=True,
    quick=True,
)
[command] - flirt -in
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/sub-02_ses-0
1_run-21669_T1w.nii.gz -ref
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/01-reorient/sub-02_ses-01_run-32679_mod-T2w_reorient.nii.gz -cost normmi
-searchcost normmi -anglerep euler -bins 256 -interp trilinear -dof 6 -out
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface/sub-02_ses-01_run-32679_mod-T2w_affine.nii.gz -omat
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface/sub-02_ses-01_run-32679_mod-T2w_affine.txt -verbose 1 -searchrx
-30 30 -searchry -30 30 -searchrz -30 30
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface/sub-02_ses-01_run-32679_mod-T2w_affine.nii.gz
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface/sub-02_ses-01_run-32679_mod-T2w_affine.txt
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applyaffine -image-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/sub-02_ses-0
1_run-21669_mod-T1w_defacemask.nii.gz -template-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/01-reorient/sub-02_ses-01_run-32679_mod-T2w_reorient.nii.gz -transform-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface/sub-02_ses-01_run-32679_mod-T2w_affine.txt -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface -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-defacing/derivatives/defacing/subjects/
sub-02/ses-01/sub-02_ses-01_run-21669_mod-T1w_defacemask.nii.gz'),
    template_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjec
ts/sub-02/ses-01/workspace_32679/01-reorient/sub-02_ses-01_run-32679_mod-T2w_reo
rient.nii.gz'),
    transform_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subje
cts/sub-02/ses-01/workspace_32679/03-deface/sub-02_ses-01_run-32679_mod-T2w_affi
ne.txt'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/workspace_32679/03-deface'),
    entities={'sub': '02', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'32679'},
    interpolation='nearestneighbour',
)
[command] - flirt -in
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/sub-02_ses-0
1_run-21669_mod-T1w_defacemask.nii.gz -ref
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/01-reorient/sub-02_ses-01_run-32679_mod-T2w_reorient.nii.gz -init
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface/sub-02_ses-01_run-32679_mod-T2w_affine.txt -interp
nearestneighbour -applyxfm -out
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface/sub-02_ses-01_run-32679_mod-T2w_applyaffine.nii.gz
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface/sub-02_ses-01_run-32679_mod-T2w_applyaffine.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applymask -image-file
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface/sub-02_ses-01_run-32679_mod-T2w_applyaffine.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface -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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/s
ub-02/ses-01/workspace_32679/03-deface/sub-02_ses-01_run-32679_mod-T2w_applyaffi
ne.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/workspace_32679/03-deface'),
    entities={'sub': '02', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'32679'},
)
[command] - fslmaths
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/01-reorient/sub-02_ses-01_run-32679_mod-T2w_reorient.nii.gz -mas
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface/sub-02_ses-01_run-32679_mod-T2w_applyaffine.nii.gz
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface/sub-02_ses-01_run-32679_mod-T2w_applymask.nii.gz
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface/sub-02_ses-01_run-32679_mod-T2w_applymask.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface maskdiff -mask1-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/02-brainmask/sub-02_ses-01_run-32679_mod-T2w_brainmask.nii.gz -mask2-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface/sub-02_ses-01_run-32679_mod-T2w_applyaffine.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/quality_chec
k -entities sub-02_modality-T2w_mod-T2w_ses-01_run-32679 -inv-mask1 False
-inv-mask2 True -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.maskdiff(
    mask1_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/workspace_32679/02-brainmask/sub-02_ses-01_run-32679_mod-T2w_brain
mask.nii.gz'),
    mask2_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/workspace_32679/03-deface/sub-02_ses-01_run-32679_mod-T2w_applyaff
ine.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/quality_check'),
    entities={'sub': '02', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'32679'},
    inv_mask1=False,
    inv_mask2=True,
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/quality_chec
k/sub-02_ses-01_run-32679_mod-T2w_maskdiff.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mean-correlation -data-files-regex
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/01-reorient/sub-02_ses-01_run-32679_mod-T2w_reorient.nii.gz -atlas-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface/sub-02_ses-01_run-32679_mod-T2w_affine.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01
-correlation-threshold None -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-defacing/derivatives/defacing/sub
jects/sub-02/ses-01/workspace_32679/01-reorient/sub-02_ses-01_run-32679_mod-T2w_
reorient.nii.gz'),
    atlas_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/workspace_32679/03-deface/sub-02_ses-01_run-32679_mod-T2w_affine.n
ii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/quality_check'),
    correlation_threshold=None,
    suffix='_T2w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/quality_chec
k/mean_correlations_T2w.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-defacing-mosaic -im-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface/sub-02_ses-01_run-32679_mod-T2w_applyaffine.nii.gz -mask-file
/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_T2w.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01 -entities
sub-02_modality-T2w_mod-T2w_ses-01_run-32679 -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_defacing_mosaic(
    im_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub
-02/ses-01/workspace_32679/03-deface/sub-02_ses-01_run-32679_mod-T2w_applyaffine
.nii.gz'),
    mask_file=PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_T
2w.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/figures'),
    entities={'sub': '02', 'modality': 'T2w', 'mod': 'T2w', 'ses': '01', 'run':
'32679'},
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/figures/sub-
02_ses-01_run-32679_mod-T2w_defacemosaic.png
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface copyfiles -source-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32
679/03-deface/sub-02_ses-01_run-32679_mod-T2w_applymask.nii.gz,/tmp/brainprep-de
facing/derivatives/defacing/subjects/sub-02/ses-01/workspace_32679/03-deface/sub
-02_ses-01_run-32679_mod-T2w_applyaffine.nii.gz,/tmp/brainprep-defacing/derivati
ves/defacing/subjects/sub-02/ses-01/workspace_32679/03-deface/sub-02_ses-01_run-
32679_mod-T2w_affine.txt,/tmp/brainprep-defacing/derivatives/defacing/subjects/s
ub-02/ses-01/quality_check/mean_correlations_T2w.tsv -destination-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/sub-02_ses-0
1_run-32679_T2w.nii.gz,/tmp/brainprep-defacing/derivatives/defacing/subjects/sub
-02/ses-01/sub-02_ses-01_run-32679_mod-T2w_defacemask.nii.gz,/tmp/brainprep-defa
cing/derivatives/defacing/subjects/sub-02/ses-01/sub-02_ses-01_run-32679_mod-T2w
_affine.txt,/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/
quality_check/sub-02_ses-01_run-32679_mod-T2w_corr.tsv -output-dir
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjec
ts/sub-02/ses-01/workspace_32679/03-deface/sub-02_ses-01_run-32679_mod-T2w_apply
mask.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/w
orkspace_32679/03-deface/sub-02_ses-01_run-32679_mod-T2w_applyaffine.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/w
orkspace_32679/03-deface/sub-02_ses-01_run-32679_mod-T2w_affine.txt'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/q
uality_check/mean_correlations_T2w.tsv')],
    destination_files=[PosixPath('/tmp/brainprep-defacing/derivatives/defacing/s
ubjects/sub-02/ses-01/sub-02_ses-01_run-32679_T2w.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/s
ub-02_ses-01_run-32679_mod-T2w_defacemask.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/s
ub-02_ses-01_run-32679_mod-T2w_affine.txt'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/q
uality_check/sub-02_ses-01_run-32679_mod-T2w_corr.tsv')],
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01'),
    move_files=False,
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface copyfiles -source-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/quality_chec
k/mean_correlations_T2w.tsv -destination-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/quality_chec
k/sub-02_ses-01_run-32679_mod-T2w_corr.tsv -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01 -move-files
True -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-defacing/derivatives/defacing/subjec
ts/sub-02/ses-01/quality_check/mean_correlations_T2w.tsv')],
    destination_files=[PosixPath('/tmp/brainprep-defacing/derivatives/defacing/s
ubjects/sub-02/ses-01/quality_check/sub-02_ses-01_run-32679_mod-T2w_corr.tsv')],
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01'),
    move_files=True,
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[title] - Subject Level Defacing done.
__________________________________________________________________0.09s, 0.00min
[title] - Group Level Defacing...
________________________________________________________________________________
[call] brainprep.workflow.defacing.brainprep_group_defacing(
    modality='T2w',
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing'),
    overlap_threshold=0.05,
    correlation_threshold=0.5,
    keep_intermediate=False,
)
[command] - brainprep interface mean-correlation -data-files-regex
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-*/ses-*/quality_check/
*mod-T2w_corr.tsv -atlas-file None -output-dir
/tmp/brainprep-defacing/derivatives/defacing -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-defacing/derivatives/defacing/sub
jects/sub-*/ses-*/quality_check/*mod-T2w_corr.tsv'),
    atlas_file=None,
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/quality_c
heck'),
    correlation_threshold=0.5,
    suffix='_T2w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/quality_check/mean_correlations_T2w
.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-histogram -table-file
/tmp/brainprep-defacing/derivatives/defacing/quality_check/mean_correlations_T2w
.tsv -col-name mean_correlation -output-dir
/tmp/brainprep-defacing/derivatives/defacing -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-defacing/derivatives/defacing/quality_c
heck/mean_correlations_T2w.tsv'),
    col_name='mean_correlation',
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/figures')
,
    bar_coords=[0.5],
    suffix='_T2w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/figures/histogram_mean_correlation_
T2w.png
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mask-overlap -maskdiff-files-regex
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-*/ses-*/quality_check/
*mod-T2w_maskdiff.tsv -output-dir /tmp/brainprep-defacing/derivatives/defacing
-overlap-threshold 0.05 -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.mask_overlap(
    maskdiff_files_regex=PosixPath('/tmp/brainprep-defacing/derivatives/defacing
/subjects/sub-*/ses-*/quality_check/*mod-T2w_maskdiff.tsv'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/quality_c
heck'),
    overlap_threshold=0.05,
    suffix='_T2w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/quality_check/mask_overlap_T2w.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-histogram -table-file
/tmp/brainprep-defacing/derivatives/defacing/quality_check/mask_overlap_T2w.tsv
-col-name overlap -output-dir /tmp/brainprep-defacing/derivatives/defacing
-bar-coords 0.05 -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-defacing/derivatives/defacing/quality_c
heck/mask_overlap_T2w.tsv'),
    col_name='overlap',
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/figures')
,
    bar_coords=[0.05],
    suffix='_T2w',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/figures/histogram_overlap_T2w.png
__________________________________________________________________0.00s, 0.00min
[title] - Group Level Defacing done.
__________________________________________________________________0.03s, 0.00min
[warn] - BIDS file name does not contain run key: sub-01_FLAIR.nii.gz
[title] - Subject Level Defacing...
________________________________________________________________________________
[call] brainprep.workflow.defacing.brainprep_defacing(
    anatomical_file=PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/su
b-01_FLAIR.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01'),
    keep_intermediate=True,
    kwargs={'entities': {'sub': '01', 'modality': 'FLAIR', 'mod': 'FLAIR',
'ses': '01', 'run': '16566'}},
)
[info] - setting workspace directory:
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/01-reorient/sub-01_ses-01_run-16566_mod-FLAIR_reorient.nii.gz -o
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/02-brainmask/sub-01_ses-01_run-16566_mod-FLAIR_brain.nii.gz -m
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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
[info] - using T1w:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/sub-01_ses-0
1_run-34706_T1w.nii.gz
[info] - using defacing mask:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/sub-01_ses-0
1_run-34706_mod-T1w_defacemask.nii.gz
[command] - brainprep interface affine -anatomical-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/sub-01_ses-0
1_run-34706_T1w.nii.gz -template-file
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface -entities sub-01_modality-FLAIR_mod-FLAIR_ses-01_run-16566 -rigid
True -quick True -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-defacing/derivatives/defacing/subj
ects/sub-01/ses-01/sub-01_ses-01_run-34706_T1w.nii.gz'),
    template_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjec
ts/sub-01/ses-01/workspace_16566/01-reorient/sub-01_ses-01_run-16566_mod-FLAIR_r
eorient.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/workspace_16566/03-deface'),
    entities={'sub': '01', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '16566'},
    rigid=True,
    quick=True,
)
[command] - flirt -in
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/sub-01_ses-0
1_run-34706_T1w.nii.gz -ref
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/01-reorient/sub-01_ses-01_run-16566_mod-FLAIR_reorient.nii.gz -cost normmi
-searchcost normmi -anglerep euler -bins 256 -interp trilinear -dof 6 -out
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_affine.nii.gz -omat
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_affine.txt -verbose 1 -searchrx
-30 30 -searchry -30 30 -searchrz -30 30
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_affine.nii.gz
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_affine.txt
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applyaffine -image-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/sub-01_ses-0
1_run-34706_mod-T1w_defacemask.nii.gz -template-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/01-reorient/sub-01_ses-01_run-16566_mod-FLAIR_reorient.nii.gz
-transform-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_affine.txt -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface -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-defacing/derivatives/defacing/subjects/
sub-01/ses-01/sub-01_ses-01_run-34706_mod-T1w_defacemask.nii.gz'),
    template_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjec
ts/sub-01/ses-01/workspace_16566/01-reorient/sub-01_ses-01_run-16566_mod-FLAIR_r
eorient.nii.gz'),
    transform_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subje
cts/sub-01/ses-01/workspace_16566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_af
fine.txt'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/workspace_16566/03-deface'),
    entities={'sub': '01', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '16566'},
    interpolation='nearestneighbour',
)
[command] - flirt -in
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/sub-01_ses-0
1_run-34706_mod-T1w_defacemask.nii.gz -ref
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/01-reorient/sub-01_ses-01_run-16566_mod-FLAIR_reorient.nii.gz -init
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_affine.txt -interp
nearestneighbour -applyxfm -out
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_applyaffine.nii.gz
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_applyaffine.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applymask -image-file
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_applyaffine.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface -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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/s
ub-01/ses-01/workspace_16566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_applyaf
fine.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/workspace_16566/03-deface'),
    entities={'sub': '01', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '16566'},
)
[command] - fslmaths
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/01-reorient/sub-01_ses-01_run-16566_mod-FLAIR_reorient.nii.gz -mas
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_applyaffine.nii.gz
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_applymask.nii.gz
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_applymask.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface maskdiff -mask1-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/02-brainmask/sub-01_ses-01_run-16566_mod-FLAIR_brainmask.nii.gz -mask2-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_applyaffine.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/quality_chec
k -entities sub-01_modality-FLAIR_mod-FLAIR_ses-01_run-16566 -inv-mask1 False
-inv-mask2 True -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.maskdiff(
    mask1_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/workspace_16566/02-brainmask/sub-01_ses-01_run-16566_mod-FLAIR_bra
inmask.nii.gz'),
    mask2_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/workspace_16566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_applya
ffine.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/quality_check'),
    entities={'sub': '01', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '16566'},
    inv_mask1=False,
    inv_mask2=True,
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/quality_chec
k/sub-01_ses-01_run-16566_mod-FLAIR_maskdiff.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mean-correlation -data-files-regex
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/01-reorient/sub-01_ses-01_run-16566_mod-FLAIR_reorient.nii.gz -atlas-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_affine.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01
-correlation-threshold None -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-defacing/derivatives/defacing/sub
jects/sub-01/ses-01/workspace_16566/01-reorient/sub-01_ses-01_run-16566_mod-FLAI
R_reorient.nii.gz'),
    atlas_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/workspace_16566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_affine
.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/quality_check'),
    correlation_threshold=None,
    suffix='_FLAIR',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/quality_chec
k/mean_correlations_FLAIR.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-defacing-mosaic -im-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_applyaffine.nii.gz -mask-file
/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_FLAIR.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01 -entities
sub-01_modality-FLAIR_mod-FLAIR_ses-01_run-16566 -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_defacing_mosaic(
    im_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub
-01/ses-01/workspace_16566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_applyaffi
ne.nii.gz'),
    mask_file=PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-01/anat/sub-01_F
LAIR.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01/figures'),
    entities={'sub': '01', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '16566'},
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/figures/sub-
01_ses-01_run-16566_mod-FLAIR_defacemosaic.png
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface copyfiles -source-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16
566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_applymask.nii.gz,/tmp/brainprep-
defacing/derivatives/defacing/subjects/sub-01/ses-01/workspace_16566/03-deface/s
ub-01_ses-01_run-16566_mod-FLAIR_applyaffine.nii.gz,/tmp/brainprep-defacing/deri
vatives/defacing/subjects/sub-01/ses-01/workspace_16566/03-deface/sub-01_ses-01_
run-16566_mod-FLAIR_affine.txt,/tmp/brainprep-defacing/derivatives/defacing/subj
ects/sub-01/ses-01/quality_check/mean_correlations_FLAIR.tsv -destination-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/sub-01_ses-0
1_run-16566_FLAIR.nii.gz,/tmp/brainprep-defacing/derivatives/defacing/subjects/s
ub-01/ses-01/sub-01_ses-01_run-16566_mod-FLAIR_defacemask.nii.gz,/tmp/brainprep-
defacing/derivatives/defacing/subjects/sub-01/ses-01/sub-01_ses-01_run-16566_mod
-FLAIR_affine.txt,/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/s
es-01/quality_check/sub-01_ses-01_run-16566_mod-FLAIR_corr.tsv -output-dir
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjec
ts/sub-01/ses-01/workspace_16566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_app
lymask.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/w
orkspace_16566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_applyaffine.nii.gz'),

PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/w
orkspace_16566/03-deface/sub-01_ses-01_run-16566_mod-FLAIR_affine.txt'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/q
uality_check/mean_correlations_FLAIR.tsv')],
    destination_files=[PosixPath('/tmp/brainprep-defacing/derivatives/defacing/s
ubjects/sub-01/ses-01/sub-01_ses-01_run-16566_FLAIR.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/s
ub-01_ses-01_run-16566_mod-FLAIR_defacemask.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/s
ub-01_ses-01_run-16566_mod-FLAIR_affine.txt'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/q
uality_check/sub-01_ses-01_run-16566_mod-FLAIR_corr.tsv')],
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01'),
    move_files=False,
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface copyfiles -source-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/quality_chec
k/mean_correlations_FLAIR.tsv -destination-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01/quality_chec
k/sub-01_ses-01_run-16566_mod-FLAIR_corr.tsv -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-01/ses-01 -move-files
True -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-defacing/derivatives/defacing/subjec
ts/sub-01/ses-01/quality_check/mean_correlations_FLAIR.tsv')],
    destination_files=[PosixPath('/tmp/brainprep-defacing/derivatives/defacing/s
ubjects/sub-01/ses-01/quality_check/sub-01_ses-01_run-16566_mod-FLAIR_corr.tsv')
],
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-01/ses-01'),
    move_files=True,
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[title] - Subject Level Defacing done.
__________________________________________________________________0.09s, 0.00min
[warn] - BIDS file name does not contain run key: sub-02_FLAIR.nii.gz
[title] - Subject Level Defacing...
________________________________________________________________________________
[call] brainprep.workflow.defacing.brainprep_defacing(
    anatomical_file=PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/su
b-02_FLAIR.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01'),
    keep_intermediate=True,
    kwargs={'entities': {'sub': '02', 'modality': 'FLAIR', 'mod': 'FLAIR',
'ses': '01', 'run': '24276'}},
)
[info] - setting workspace directory:
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/01-reorient/sub-02_ses-01_run-24276_mod-FLAIR_reorient.nii.gz -o
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/02-brainmask/sub-02_ses-01_run-24276_mod-FLAIR_brain.nii.gz -m
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/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
[info] - using T1w:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/sub-02_ses-0
1_run-21669_T1w.nii.gz
[info] - using defacing mask:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/sub-02_ses-0
1_run-21669_mod-T1w_defacemask.nii.gz
[command] - brainprep interface affine -anatomical-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/sub-02_ses-0
1_run-21669_T1w.nii.gz -template-file
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface -entities sub-02_modality-FLAIR_mod-FLAIR_ses-01_run-24276 -rigid
True -quick True -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-defacing/derivatives/defacing/subj
ects/sub-02/ses-01/sub-02_ses-01_run-21669_T1w.nii.gz'),
    template_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjec
ts/sub-02/ses-01/workspace_24276/01-reorient/sub-02_ses-01_run-24276_mod-FLAIR_r
eorient.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/workspace_24276/03-deface'),
    entities={'sub': '02', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '24276'},
    rigid=True,
    quick=True,
)
[command] - flirt -in
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/sub-02_ses-0
1_run-21669_T1w.nii.gz -ref
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/01-reorient/sub-02_ses-01_run-24276_mod-FLAIR_reorient.nii.gz -cost normmi
-searchcost normmi -anglerep euler -bins 256 -interp trilinear -dof 6 -out
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_affine.nii.gz -omat
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_affine.txt -verbose 1 -searchrx
-30 30 -searchry -30 30 -searchrz -30 30
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_affine.nii.gz
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_affine.txt
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applyaffine -image-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/sub-02_ses-0
1_run-21669_mod-T1w_defacemask.nii.gz -template-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/01-reorient/sub-02_ses-01_run-24276_mod-FLAIR_reorient.nii.gz
-transform-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_affine.txt -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface -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-defacing/derivatives/defacing/subjects/
sub-02/ses-01/sub-02_ses-01_run-21669_mod-T1w_defacemask.nii.gz'),
    template_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjec
ts/sub-02/ses-01/workspace_24276/01-reorient/sub-02_ses-01_run-24276_mod-FLAIR_r
eorient.nii.gz'),
    transform_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subje
cts/sub-02/ses-01/workspace_24276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_af
fine.txt'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/workspace_24276/03-deface'),
    entities={'sub': '02', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '24276'},
    interpolation='nearestneighbour',
)
[command] - flirt -in
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/sub-02_ses-0
1_run-21669_mod-T1w_defacemask.nii.gz -ref
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/01-reorient/sub-02_ses-01_run-24276_mod-FLAIR_reorient.nii.gz -init
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_affine.txt -interp
nearestneighbour -applyxfm -out
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_applyaffine.nii.gz
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_applyaffine.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface applymask -image-file
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_applyaffine.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface -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-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjects/s
ub-02/ses-01/workspace_24276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_applyaf
fine.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/workspace_24276/03-deface'),
    entities={'sub': '02', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '24276'},
)
[command] - fslmaths
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/01-reorient/sub-02_ses-01_run-24276_mod-FLAIR_reorient.nii.gz -mas
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_applyaffine.nii.gz
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_applymask.nii.gz
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_applymask.nii.gz
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface maskdiff -mask1-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/02-brainmask/sub-02_ses-01_run-24276_mod-FLAIR_brainmask.nii.gz -mask2-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_applyaffine.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/quality_chec
k -entities sub-02_modality-FLAIR_mod-FLAIR_ses-01_run-24276 -inv-mask1 False
-inv-mask2 True -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.maskdiff(
    mask1_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/workspace_24276/02-brainmask/sub-02_ses-01_run-24276_mod-FLAIR_bra
inmask.nii.gz'),
    mask2_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/workspace_24276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_applya
ffine.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/quality_check'),
    entities={'sub': '02', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '24276'},
    inv_mask1=False,
    inv_mask2=True,
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/quality_chec
k/sub-02_ses-01_run-24276_mod-FLAIR_maskdiff.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mean-correlation -data-files-regex
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/01-reorient/sub-02_ses-01_run-24276_mod-FLAIR_reorient.nii.gz -atlas-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_affine.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01
-correlation-threshold None -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-defacing/derivatives/defacing/sub
jects/sub-02/ses-01/workspace_24276/01-reorient/sub-02_ses-01_run-24276_mod-FLAI
R_reorient.nii.gz'),
    atlas_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/workspace_24276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_affine
.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/quality_check'),
    correlation_threshold=None,
    suffix='_FLAIR',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/quality_chec
k/mean_correlations_FLAIR.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-defacing-mosaic -im-file
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_applyaffine.nii.gz -mask-file
/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_FLAIR.nii.gz -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01 -entities
sub-02_modality-FLAIR_mod-FLAIR_ses-01_run-24276 -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_defacing_mosaic(
    im_file=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub
-02/ses-01/workspace_24276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_applyaffi
ne.nii.gz'),
    mask_file=PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-01/anat/sub-02_F
LAIR.nii.gz'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01/figures'),
    entities={'sub': '02', 'modality': 'FLAIR', 'mod': 'FLAIR', 'ses': '01',
'run': '24276'},
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/figures/sub-
02_ses-01_run-24276_mod-FLAIR_defacemosaic.png
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface copyfiles -source-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24
276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_applymask.nii.gz,/tmp/brainprep-
defacing/derivatives/defacing/subjects/sub-02/ses-01/workspace_24276/03-deface/s
ub-02_ses-01_run-24276_mod-FLAIR_applyaffine.nii.gz,/tmp/brainprep-defacing/deri
vatives/defacing/subjects/sub-02/ses-01/workspace_24276/03-deface/sub-02_ses-01_
run-24276_mod-FLAIR_affine.txt,/tmp/brainprep-defacing/derivatives/defacing/subj
ects/sub-02/ses-01/quality_check/mean_correlations_FLAIR.tsv -destination-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/sub-02_ses-0
1_run-24276_FLAIR.nii.gz,/tmp/brainprep-defacing/derivatives/defacing/subjects/s
ub-02/ses-01/sub-02_ses-01_run-24276_mod-FLAIR_defacemask.nii.gz,/tmp/brainprep-
defacing/derivatives/defacing/subjects/sub-02/ses-01/sub-02_ses-01_run-24276_mod
-FLAIR_affine.txt,/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/s
es-01/quality_check/sub-02_ses-01_run-24276_mod-FLAIR_corr.tsv -output-dir
/tmp/brainprep-defacing/derivatives/defacing/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-defacing/derivatives/defacing/subjec
ts/sub-02/ses-01/workspace_24276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_app
lymask.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/w
orkspace_24276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_applyaffine.nii.gz'),

PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/w
orkspace_24276/03-deface/sub-02_ses-01_run-24276_mod-FLAIR_affine.txt'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/q
uality_check/mean_correlations_FLAIR.tsv')],
    destination_files=[PosixPath('/tmp/brainprep-defacing/derivatives/defacing/s
ubjects/sub-02/ses-01/sub-02_ses-01_run-24276_FLAIR.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/s
ub-02_ses-01_run-24276_mod-FLAIR_defacemask.nii.gz'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/s
ub-02_ses-01_run-24276_mod-FLAIR_affine.txt'),
PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/q
uality_check/sub-02_ses-01_run-24276_mod-FLAIR_corr.tsv')],
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01'),
    move_files=False,
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface copyfiles -source-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/quality_chec
k/mean_correlations_FLAIR.tsv -destination-files
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01/quality_chec
k/sub-02_ses-01_run-24276_mod-FLAIR_corr.tsv -output-dir
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-02/ses-01 -move-files
True -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-defacing/derivatives/defacing/subjec
ts/sub-02/ses-01/quality_check/mean_correlations_FLAIR.tsv')],
    destination_files=[PosixPath('/tmp/brainprep-defacing/derivatives/defacing/s
ubjects/sub-02/ses-01/quality_check/sub-02_ses-01_run-24276_mod-FLAIR_corr.tsv')
],
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/subjects/
sub-02/ses-01'),
    move_files=True,
    dryrun=True,
)
__________________________________________________________________0.00s, 0.00min
[title] - Subject Level Defacing done.
__________________________________________________________________0.09s, 0.00min
[title] - Group Level Defacing...
________________________________________________________________________________
[call] brainprep.workflow.defacing.brainprep_group_defacing(
    modality='FLAIR',
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing'),
    overlap_threshold=0.05,
    correlation_threshold=0.5,
    keep_intermediate=False,
)
[command] - brainprep interface mean-correlation -data-files-regex
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-*/ses-*/quality_check/
*mod-FLAIR_corr.tsv -atlas-file None -output-dir
/tmp/brainprep-defacing/derivatives/defacing -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-defacing/derivatives/defacing/sub
jects/sub-*/ses-*/quality_check/*mod-FLAIR_corr.tsv'),
    atlas_file=None,
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/quality_c
heck'),
    correlation_threshold=0.5,
    suffix='_FLAIR',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/quality_check/mean_correlations_FLA
IR.tsv
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-histogram -table-file
/tmp/brainprep-defacing/derivatives/defacing/quality_check/mean_correlations_FLA
IR.tsv -col-name mean_correlation -output-dir
/tmp/brainprep-defacing/derivatives/defacing -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-defacing/derivatives/defacing/quality_c
heck/mean_correlations_FLAIR.tsv'),
    col_name='mean_correlation',
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/figures')
,
    bar_coords=[0.5],
    suffix='_FLAIR',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/figures/histogram_mean_correlation_
FLAIR.png
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface mask-overlap -maskdiff-files-regex
/tmp/brainprep-defacing/derivatives/defacing/subjects/sub-*/ses-*/quality_check/
*mod-FLAIR_maskdiff.tsv -output-dir /tmp/brainprep-defacing/derivatives/defacing
-overlap-threshold 0.05 -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.mask_overlap(
    maskdiff_files_regex=PosixPath('/tmp/brainprep-defacing/derivatives/defacing
/subjects/sub-*/ses-*/quality_check/*mod-FLAIR_maskdiff.tsv'),
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/quality_c
heck'),
    overlap_threshold=0.05,
    suffix='_FLAIR',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/quality_check/mask_overlap_FLAIR.ts
v
__________________________________________________________________0.00s, 0.00min
[command] - brainprep interface plot-histogram -table-file
/tmp/brainprep-defacing/derivatives/defacing/quality_check/mask_overlap_FLAIR.ts
v -col-name overlap -output-dir /tmp/brainprep-defacing/derivatives/defacing
-bar-coords 0.05 -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-defacing/derivatives/defacing/quality_c
heck/mask_overlap_FLAIR.tsv'),
    col_name='overlap',
    output_dir=PosixPath('/tmp/brainprep-defacing/derivatives/defacing/figures')
,
    bar_coords=[0.05],
    suffix='_FLAIR',
    dryrun=True,
)
[info] - checking output:
/tmp/brainprep-defacing/derivatives/defacing/figures/histogram_overlap_FLAIR.png
__________________________________________________________________0.00s, 0.00min
[title] - Group Level Defacing done.
__________________________________________________________________0.03s, 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-defacing",
            "--anatomical_file", str(subject_data.anat),
            "--output-dir", str(outdir),
            "--keep-intermediate",
        ]
        for subject_data in data["T1w"].values()
    ]
)
commands.append(
    [
        [
            "brainprep", "subject-level-defacing",
            "--anatomical_file", str(subject_data.anat),
            "--output-dir", str(outdir),
            "--keep-intermediate",
        ]
        for mod in ("T2w", "FLAIR")
        for subject_data in data[mod].values()
    ]
)
commands.append(
    [
        [
            "brainprep", "group-level-defacing",
            "--modality", modality,
            "--output-dir", str(outdir),
        ]
        for modality in data.keys()
    ]
)
pprint(commands)

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

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: 153 MB