Note

Go to the end to download the full example code.

SBM

Simple example.

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

Data

Let’s first get some anatomical data.

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

datadir = Path("/tmp/brainprep-data")
datadir.mkdir(parents=True, exist_ok=True)
dataset = OpenMSDataset(datadir)
data = Bunch(
    sub01=dataset.fetch(
        subject="01",
        modality="T1w",
        dtype="longitudinal",
    ),
    sub02=dataset.fetch(
        subject="02",
        modality="T1w",
        dtype="longitudinal",
    ),
)
print(data)

[info] - downloading:
https://raw.githubusercontent.com/muschellij2/open_ms_data/refs/heads/master/lon
gitudinal/raw/patient01/study1_T1W.nii.gz
[info] - downloading:
https://raw.githubusercontent.com/muschellij2/open_ms_data/refs/heads/master/lon
gitudinal/raw/patient01/study2_T1W.nii.gz
[info] - downloading:
https://raw.githubusercontent.com/muschellij2/open_ms_data/refs/heads/master/lon
gitudinal/raw/patient02/study1_T1W.nii.gz
[info] - downloading:
https://raw.githubusercontent.com/muschellij2/open_ms_data/refs/heads/master/lon
gitudinal/raw/patient02/study2_T1W.nii.gz
Bunch(
  sub01: Bunch(
    description: PosixPath('/tmp/brainprep-data/rawdata/dataset_description.json')
    anat1: PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-study1/anat/sub-01_ses-study1_T1w.nii.gz')
    anat2: PosixPath('/tmp/brainprep-data/rawdata/sub-01/ses-study2/anat/sub-01_ses-study2_T1w.nii.gz')
  )
  sub02: Bunch(
    description: PosixPath('/tmp/brainprep-data/rawdata/dataset_description.json')
    anat1: PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-study1/anat/sub-02_ses-study1_T1w.nii.gz')
    anat2: PosixPath('/tmp/brainprep-data/rawdata/sub-02/ses-study2/anat/sub-02_ses-study2_T1w.nii.gz')
  )
)

Analysis

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

from brainprep.workflow import (
    brainprep_sbm,
    brainprep_group_sbm,
    brainprep_longitudinal_sbm,
)
from brainprep.config import Config
from brainprep.reporting import RSTReport

outdir = Path("/tmp/brainprep-sbm")
outdir.mkdir(parents=True, exist_ok=True)
with Config(dryrun=True, verbose=True):
    for subject_data in data.values():
        for t1_file in [subject_data.anat1, subject_data.anat2]:
            outputs = brainprep_sbm(
                t1_file=t1_file,
                output_dir=outdir,
                do_lgi=True,
                wm_file=(datadir / "deprecated"),
                keep_intermediate=True,
            )
            (outputs.subject_dir / "stats").mkdir(parents=True, exist_ok=True)
            (outputs.subject_dir / "stats" / "lh.aparc.stats").touch(
                exist_ok=True
            )
    outputs = brainprep_group_sbm(
        output_dir=outdir,
        euler_threshold=-217,
        keep_intermediate=True,
    )
    outputs = brainprep_longitudinal_sbm(
        t1_files=[subject_data.anat1, subject_data.anat2],
        output_dir=outdir,
        keep_intermediate=True,
    )
    for subject_dir in outputs.subject_dirs:
        (subject_dir / "stats").mkdir(parents=True, exist_ok=True)
        (subject_dir / "stats" / "lh.aparc.stats").touch(exist_ok=True)
    outputs = brainprep_group_sbm(
        output_dir=outdir,
        euler_threshold=-217,
        longitudinal=True,
        keep_intermediate=True,
    )

[warn] - BIDS file name does not contain run key: sub-01_ses-study1_T1w.nii.gz
[title] - Subject Level SBM...
[info] - setting workspace directory:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/workspace
[deprecated] - You passed a white matter file as input. This behavior is
deprecated and will be removed in version >1.
[command] - recon-all -all -subjid run-15456 -i
/tmp/brainprep-data/rawdata/sub-01/ses-study1/anat/sub-01_ses-study1_T1w.nii.gz
-sd /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1 -noappend
-no-isrunning
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/scripts/
recon-all.log
[command] - recon-all -localGI -subjid run-15456 -sd
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1 -no-isrunning
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
pial_lgi
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
pial_lgi
[command] - xhemireg --s run-15456
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/xh
emireg.lh.log
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/xh
emireg.rh.log
[command] - surfreg --s run-15456 --lh --t fsaverage_sym --no-annot
[command] - surfreg --s run-15456 --lh --t fsaverage_sym --no-annot --xhemi
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
fsaverage_sym.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
thickness
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
thickness --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
thickness.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
thickness.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
thickness
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
thickness --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
thickness.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
thickness.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
curv
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
curv --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
curv.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
curv.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
curv
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
curv --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
curv.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
curv.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
area
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
area --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
area.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
area.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
area
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
area --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
area.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
area.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
pial_lgi
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
pial_lgi --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
pial_lgi.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
pial_lgi.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
pial_lgi
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
pial_lgi --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
pial_lgi.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
pial_lgi.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
sulc
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
sulc --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
sulc.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
sulc.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
sulc
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
sulc --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
sulc.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
sulc.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
thickness.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
thickness.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
curv.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
curv.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
area.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
area.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
pial_lgi.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
pial_lgi.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/lh.
sulc.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/surf/rh.
sulc.fsaverage_sym.mgh
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/apar
c+aseg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/apar
c+aseg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/apar
c+aseg.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/apar
c.a2009s+aseg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/apar
c.a2009s+aseg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/apar
c.a2009s+aseg.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/aseg
.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/aseg
.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/aseg
.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/wm.m
gz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/wm.n
ii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/wm.n
ii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/ribb
on.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/ribb
on.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/ribb
on.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/brai
n.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/brai
n.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/run-15456/mri/brai
n.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/workspace/wm_run-1
5456.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/workspace/gm_run-1
5456.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/workspace/csf_run-
15456.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/workspace/brain_ru
n-15456.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study1/figures/sub-01_ses
-study1_run-15456_brainparc.png
[title] - Subject Level SBM done.
[warn] - BIDS file name does not contain run key: sub-01_ses-study2_T1w.nii.gz
[title] - Subject Level SBM...
[info] - setting workspace directory:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/workspace
[deprecated] - You passed a white matter file as input. This behavior is
deprecated and will be removed in version >1.
[command] - recon-all -all -subjid run-27245 -i
/tmp/brainprep-data/rawdata/sub-01/ses-study2/anat/sub-01_ses-study2_T1w.nii.gz
-sd /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2 -noappend
-no-isrunning
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/scripts/
recon-all.log
[command] - recon-all -localGI -subjid run-27245 -sd
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2 -no-isrunning
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
pial_lgi
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
pial_lgi
[command] - xhemireg --s run-27245
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/xh
emireg.lh.log
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/xh
emireg.rh.log
[command] - surfreg --s run-27245 --lh --t fsaverage_sym --no-annot
[command] - surfreg --s run-27245 --lh --t fsaverage_sym --no-annot --xhemi
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
fsaverage_sym.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
thickness
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
thickness --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
thickness.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
thickness.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
thickness
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
thickness --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
thickness.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
thickness.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
curv
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
curv --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
curv.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
curv.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
curv
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
curv --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
curv.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
curv.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
area
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
area --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
area.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
area.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
area
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
area --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
area.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
area.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
pial_lgi
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
pial_lgi --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
pial_lgi.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
pial_lgi.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
pial_lgi
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
pial_lgi --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
pial_lgi.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
pial_lgi.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
sulc
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
sulc --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
sulc.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
sulc.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
sulc
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
sulc --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
sulc.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
sulc.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
thickness.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
thickness.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
curv.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
curv.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
area.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
area.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
pial_lgi.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
pial_lgi.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/lh.
sulc.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/surf/rh.
sulc.fsaverage_sym.mgh
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/apar
c+aseg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/apar
c+aseg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/apar
c+aseg.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/apar
c.a2009s+aseg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/apar
c.a2009s+aseg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/apar
c.a2009s+aseg.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/aseg
.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/aseg
.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/aseg
.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/wm.m
gz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/wm.n
ii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/wm.n
ii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/ribb
on.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/ribb
on.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/ribb
on.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/brai
n.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/brai
n.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/run-27245/mri/brai
n.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/workspace/wm_run-2
7245.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/workspace/gm_run-2
7245.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/workspace/csf_run-
27245.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/workspace/brain_ru
n-27245.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-01/ses-study2/figures/sub-01_ses
-study2_run-27245_brainparc.png
[title] - Subject Level SBM done.
[warn] - BIDS file name does not contain run key: sub-02_ses-study1_T1w.nii.gz
[title] - Subject Level SBM...
[info] - setting workspace directory:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/workspace
[deprecated] - You passed a white matter file as input. This behavior is
deprecated and will be removed in version >1.
[command] - recon-all -all -subjid run-38141 -i
/tmp/brainprep-data/rawdata/sub-02/ses-study1/anat/sub-02_ses-study1_T1w.nii.gz
-sd /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1 -noappend
-no-isrunning
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/scripts/
recon-all.log
[command] - recon-all -localGI -subjid run-38141 -sd
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1 -no-isrunning
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
pial_lgi
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
pial_lgi
[command] - xhemireg --s run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/xh
emireg.lh.log
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/xh
emireg.rh.log
[command] - surfreg --s run-38141 --lh --t fsaverage_sym --no-annot
[command] - surfreg --s run-38141 --lh --t fsaverage_sym --no-annot --xhemi
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
fsaverage_sym.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
thickness
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
thickness --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
thickness.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
thickness.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
thickness
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
thickness --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
thickness.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
thickness.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
curv
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
curv --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
curv.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
curv.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
curv
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
curv --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
curv.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
curv.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
area
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
area --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
area.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
area.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
area
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
area --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
area.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
area.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
pial_lgi
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
pial_lgi --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
pial_lgi.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
pial_lgi.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
pial_lgi
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
pial_lgi --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
pial_lgi.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
pial_lgi.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
sulc
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
sulc --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
sulc.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
sulc.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
sulc
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
sulc --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
sulc.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
sulc.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
thickness.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
thickness.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
curv.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
curv.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
area.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
area.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
pial_lgi.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
pial_lgi.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/lh.
sulc.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/surf/rh.
sulc.fsaverage_sym.mgh
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/apar
c+aseg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/apar
c+aseg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/apar
c+aseg.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/apar
c.a2009s+aseg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/apar
c.a2009s+aseg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/apar
c.a2009s+aseg.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/aseg
.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/aseg
.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/aseg
.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/wm.m
gz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/wm.n
ii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/wm.n
ii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/ribb
on.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/ribb
on.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/ribb
on.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/brai
n.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/brai
n.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/run-38141/mri/brai
n.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/workspace/wm_run-3
8141.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/workspace/gm_run-3
8141.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/workspace/csf_run-
38141.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/workspace/brain_ru
n-38141.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study1/figures/sub-02_ses
-study1_run-38141_brainparc.png
[title] - Subject Level SBM done.
[warn] - BIDS file name does not contain run key: sub-02_ses-study2_T1w.nii.gz
[title] - Subject Level SBM...
[info] - setting workspace directory:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/workspace
[deprecated] - You passed a white matter file as input. This behavior is
deprecated and will be removed in version >1.
[command] - recon-all -all -subjid run-13661 -i
/tmp/brainprep-data/rawdata/sub-02/ses-study2/anat/sub-02_ses-study2_T1w.nii.gz
-sd /tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2 -noappend
-no-isrunning
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/scripts/
recon-all.log
[command] - recon-all -localGI -subjid run-13661 -sd
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2 -no-isrunning
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
pial_lgi
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
pial_lgi
[command] - xhemireg --s run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/xh
emireg.lh.log
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/xh
emireg.rh.log
[command] - surfreg --s run-13661 --lh --t fsaverage_sym --no-annot
[command] - surfreg --s run-13661 --lh --t fsaverage_sym --no-annot --xhemi
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
fsaverage_sym.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
thickness
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
thickness --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
thickness.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
thickness.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
thickness
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
thickness --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
thickness.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
thickness.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
curv
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
curv --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
curv.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
curv.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
curv
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
curv --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
curv.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
curv.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
area
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
area --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
area.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
area.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
area
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
area --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
area.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
area.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
pial_lgi
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
pial_lgi --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
pial_lgi.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
pial_lgi.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
pial_lgi
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
pial_lgi --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
pial_lgi.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
pial_lgi.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
sulc
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
sulc --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
sulc.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
sulc.fsaverage_sym.mgh
[warn] - feature missing:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
sulc
[command] - mris_apply_reg --src
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
sulc --trg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
sulc.fsaverage_sym.mgh --streg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/xhemi/su
rf/lh.fsaverage_sym.sphere.reg
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/fsaverage_sym/surf
/lh.sphere.reg
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
sulc.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
thickness.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
thickness.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
curv.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
curv.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
area.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
area.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
pial_lgi.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
pial_lgi.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/lh.
sulc.fsaverage_sym.mgh
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/surf/rh.
sulc.fsaverage_sym.mgh
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/apar
c+aseg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/apar
c+aseg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/apar
c+aseg.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/apar
c.a2009s+aseg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/apar
c.a2009s+aseg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/apar
c.a2009s+aseg.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/aseg
.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/aseg
.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/aseg
.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/wm.m
gz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/wm.n
ii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/wm.n
ii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/ribb
on.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/ribb
on.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/ribb
on.nii.gz
[command] - mri_convert --resample_type nearest --reslice_like
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/rawa
vg.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/brai
n.mgz
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/brai
n.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/run-13661/mri/brai
n.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/workspace/wm_run-1
3661.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/workspace/gm_run-1
3661.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/workspace/csf_run-
13661.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/workspace/brain_ru
n-13661.nii.gz
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/subjects/sub-02/ses-study2/figures/sub-02_ses
-study2_run-13661_brainparc.png
[title] - Subject Level SBM done.
[title] - Group Level SBM...
[info] - setting workspace directory:
/tmp/brainprep-sbm/derivatives/sbm/workspace
[command] - aparcstats2table --hemi lh --meas area --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-are
a_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas area
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-area_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-are
a_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-area_stats.csv
[command] - aparcstats2table --hemi lh --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-vol
ume_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas volume
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-volume_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-vol
ume_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-volume_stats.csv
[command] - aparcstats2table --hemi lh --meas thickness --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-thi
ckness_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas thickness
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-01_run-27245 sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-thi
ckness_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-thickness_stats.csv
[command] - aparcstats2table --hemi lh --meas thicknessstd --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-thi
cknessstd_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas thicknessstd
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-01_run-27245 sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-thi
cknessstd_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-thicknessstd_stats.csv
[command] - aparcstats2table --hemi lh --meas meancurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-mea
ncurv_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas meancurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-meancurv_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-mea
ncurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-meancurv_stats.csv
[command] - aparcstats2table --hemi lh --meas gauscurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-gau
scurv_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas gauscurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-gauscurv_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-gau
scurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-gauscurv_stats.csv
[command] - aparcstats2table --hemi lh --meas foldind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-fol
dind_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas foldind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-foldind_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-fol
dind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-foldind_stats.csv
[command] - aparcstats2table --hemi lh --meas curvind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-cur
vind_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas curvind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-curvind_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-lh_meas-cur
vind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-lh_mea
s-curvind_stats.csv
[command] - aparcstats2table --hemi rh --meas area --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-are
a_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas area
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-area_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-are
a_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-area_stats.csv
[command] - aparcstats2table --hemi rh --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-vol
ume_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas volume
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-volume_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-vol
ume_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-volume_stats.csv
[command] - aparcstats2table --hemi rh --meas thickness --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-thi
ckness_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas thickness
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-01_run-27245 sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-thi
ckness_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-thickness_stats.csv
[command] - aparcstats2table --hemi rh --meas thicknessstd --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-thi
cknessstd_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas thicknessstd
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-01_run-27245 sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-thi
cknessstd_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-thicknessstd_stats.csv
[command] - aparcstats2table --hemi rh --meas meancurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-mea
ncurv_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas meancurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-meancurv_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-mea
ncurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-meancurv_stats.csv
[command] - aparcstats2table --hemi rh --meas gauscurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-gau
scurv_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas gauscurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-gauscurv_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-gau
scurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-gauscurv_stats.csv
[command] - aparcstats2table --hemi rh --meas foldind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-fol
dind_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas foldind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-foldind_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-fol
dind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-foldind_stats.csv
[command] - aparcstats2table --hemi rh --meas curvind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-cur
vind_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas curvind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-curvind_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-27245
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study2_hemi-rh_meas-cur
vind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study2_hemi-rh_mea
s-curvind_stats.csv
[command] - asegstats2table --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aseg_ses-study2_stats.csv
--delimiter comma --subjects sub-01_run-27245 sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aseg_ses-study2_stats.csv
[command] - aparcstats2table --hemi lh --meas area --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-are
a_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas area
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-area_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-are
a_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-area_stats.csv
[command] - aparcstats2table --hemi lh --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-vol
ume_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas volume
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-volume_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-vol
ume_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-volume_stats.csv
[command] - aparcstats2table --hemi lh --meas thickness --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-thi
ckness_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas thickness
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-01_run-15456 sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-thi
ckness_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-thickness_stats.csv
[command] - aparcstats2table --hemi lh --meas thicknessstd --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-thi
cknessstd_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas thicknessstd
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-01_run-15456 sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-thi
cknessstd_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-thicknessstd_stats.csv
[command] - aparcstats2table --hemi lh --meas meancurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-mea
ncurv_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas meancurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-meancurv_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-mea
ncurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-meancurv_stats.csv
[command] - aparcstats2table --hemi lh --meas gauscurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-gau
scurv_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas gauscurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-gauscurv_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-gau
scurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-gauscurv_stats.csv
[command] - aparcstats2table --hemi lh --meas foldind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-fol
dind_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas foldind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-foldind_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-fol
dind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-foldind_stats.csv
[command] - aparcstats2table --hemi lh --meas curvind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-cur
vind_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas curvind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-curvind_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-lh_meas-cur
vind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-lh_mea
s-curvind_stats.csv
[command] - aparcstats2table --hemi rh --meas area --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-are
a_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas area
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-area_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-are
a_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-area_stats.csv
[command] - aparcstats2table --hemi rh --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-vol
ume_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas volume
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-volume_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-vol
ume_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-volume_stats.csv
[command] - aparcstats2table --hemi rh --meas thickness --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-thi
ckness_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas thickness
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-01_run-15456 sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-thi
ckness_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-thickness_stats.csv
[command] - aparcstats2table --hemi rh --meas thicknessstd --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-thi
cknessstd_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas thicknessstd
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-01_run-15456 sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-thi
cknessstd_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-thicknessstd_stats.csv
[command] - aparcstats2table --hemi rh --meas meancurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-mea
ncurv_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas meancurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-meancurv_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-mea
ncurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-meancurv_stats.csv
[command] - aparcstats2table --hemi rh --meas gauscurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-gau
scurv_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas gauscurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-gauscurv_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-gau
scurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-gauscurv_stats.csv
[command] - aparcstats2table --hemi rh --meas foldind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-fol
dind_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas foldind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-foldind_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-fol
dind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-foldind_stats.csv
[command] - aparcstats2table --hemi rh --meas curvind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-cur
vind_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas curvind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-curvind_stats.csv --delimiter comma --parcid-only --subjects sub-01_run-15456
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc_ses-study1_hemi-rh_meas-cur
vind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aparc2009s_ses-study1_hemi-rh_mea
s-curvind_stats.csv
[command] - asegstats2table --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aseg_ses-study1_stats.csv
--delimiter comma --subjects sub-01_run-15456 sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/morphometry/aseg_ses-study1_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/quality_check/euler_numbers.tsv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/figures/histogram_euler_number.png
[title] - Group Level SBM done.
[warn] - BIDS file name does not contain run key: sub-02_ses-study1_T1w.nii.gz
[warn] - BIDS file name does not contain run key: sub-02_ses-study2_T1w.nii.gz
[title] - Longitudinal SBM...
[info] - setting workspace directory:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/workspace
[command] - recon-all -base sub-02_template_ses-study1:study2 -tp
sub-02_ses-study1_run-38141 -tp sub-02_ses-study2_run-13661 -all -sd
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02
[command] - recon-all -long sub-02_ses-study1_run-38141
sub-02_template_ses-study1:study2 -all -sd
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02
[command] - recon-all -long sub-02_ses-study2_run-13661
sub-02_template_ses-study1:study2 -all -sd
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/sub-02_template_
ses-study1:study2/scripts/recon-all.log
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/sub-02_ses-study
1_run-38141.long.sub-02_template_ses-study1:study2/scripts/recon-all.log
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/sub-02_ses-study
2_run-13661.long.sub-02_template_ses-study1:study2/scripts/recon-all.log
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/ses-study1/run-3
8141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/ses-study2/run-1
3661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/subjects/sub-02/template
[title] - Longitudinal SBM done.
[title] - Group Level SBM...
[info] - setting workspace directory:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/workspace
[command] - aparcstats2table --hemi lh --meas area --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-area_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas area
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-area_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-area_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-area_stats.csv
[command] - aparcstats2table --hemi lh --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-volume_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas volume
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-volume_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-volume_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-volume_stats.csv
[command] - aparcstats2table --hemi lh --meas thickness --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas thickness
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-thickness_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-thickness_stats.csv
[command] - aparcstats2table --hemi lh --meas thicknessstd --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas thicknessstd
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-thicknessstd_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-thicknessstd_stats.csv
[command] - aparcstats2table --hemi lh --meas meancurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-meancurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas meancurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-meancurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-meancurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-meancurv_stats.csv
[command] - aparcstats2table --hemi lh --meas gauscurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-gauscurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas gauscurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-gauscurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-gauscurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-gauscurv_stats.csv
[command] - aparcstats2table --hemi lh --meas foldind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-foldind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas foldind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-foldind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-foldind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-foldind_stats.csv
[command] - aparcstats2table --hemi lh --meas curvind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-curvind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas curvind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-curvind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-lh_meas-curvind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-lh_meas-curvind_stats.csv
[command] - aparcstats2table --hemi rh --meas area --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-area_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas area
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-area_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-area_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-area_stats.csv
[command] - aparcstats2table --hemi rh --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-volume_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas volume
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-volume_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-volume_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-volume_stats.csv
[command] - aparcstats2table --hemi rh --meas thickness --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas thickness
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-thickness_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-thickness_stats.csv
[command] - aparcstats2table --hemi rh --meas thicknessstd --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas thicknessstd
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-thicknessstd_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-thicknessstd_stats.csv
[command] - aparcstats2table --hemi rh --meas meancurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-meancurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas meancurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-meancurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-meancurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-meancurv_stats.csv
[command] - aparcstats2table --hemi rh --meas gauscurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-gauscurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas gauscurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-gauscurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-gauscurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-gauscurv_stats.csv
[command] - aparcstats2table --hemi rh --meas foldind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-foldind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas foldind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-foldind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-foldind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-foldind_stats.csv
[command] - aparcstats2table --hemi rh --meas curvind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-curvind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas curvind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-curvind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study2_hem
i-rh_meas-curvind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
2_hemi-rh_meas-curvind_stats.csv
[command] - asegstats2table --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aseg_ses-study2_stat
s.csv --delimiter comma --subjects sub-02_run-13661
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aseg_ses-study2_stat
s.csv
[command] - aparcstats2table --hemi lh --meas area --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-area_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas area
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-area_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-area_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-area_stats.csv
[command] - aparcstats2table --hemi lh --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-volume_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas volume
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-volume_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-volume_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-volume_stats.csv
[command] - aparcstats2table --hemi lh --meas thickness --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas thickness
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-thickness_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-thickness_stats.csv
[command] - aparcstats2table --hemi lh --meas thicknessstd --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas thicknessstd
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-thicknessstd_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-thicknessstd_stats.csv
[command] - aparcstats2table --hemi lh --meas meancurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-meancurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas meancurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-meancurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-meancurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-meancurv_stats.csv
[command] - aparcstats2table --hemi lh --meas gauscurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-gauscurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas gauscurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-gauscurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-gauscurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-gauscurv_stats.csv
[command] - aparcstats2table --hemi lh --meas foldind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-foldind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas foldind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-foldind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-foldind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-foldind_stats.csv
[command] - aparcstats2table --hemi lh --meas curvind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-curvind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi lh --meas curvind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-curvind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-lh_meas-curvind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-lh_meas-curvind_stats.csv
[command] - aparcstats2table --hemi rh --meas area --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-area_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas area
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-area_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-area_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-area_stats.csv
[command] - aparcstats2table --hemi rh --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-volume_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas volume
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-volume_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-volume_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-volume_stats.csv
[command] - aparcstats2table --hemi rh --meas thickness --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas thickness
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-thickness_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-thickness_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-thickness_stats.csv
[command] - aparcstats2table --hemi rh --meas thicknessstd --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas thicknessstd
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-thicknessstd_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-thicknessstd_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-thicknessstd_stats.csv
[command] - aparcstats2table --hemi rh --meas meancurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-meancurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas meancurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-meancurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-meancurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-meancurv_stats.csv
[command] - aparcstats2table --hemi rh --meas gauscurv --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-gauscurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas gauscurv
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-gauscurv_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-gauscurv_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-gauscurv_stats.csv
[command] - aparcstats2table --hemi rh --meas foldind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-foldind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas foldind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-foldind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-foldind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-foldind_stats.csv
[command] - aparcstats2table --hemi rh --meas curvind --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-curvind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[command] - aparcstats2table --parc aparc.a2009s --hemi rh --meas curvind
--tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-curvind_stats.csv --delimiter comma --parcid-only --subjects
sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc_ses-study1_hem
i-rh_meas-curvind_stats.csv
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aparc2009s_ses-study
1_hemi-rh_meas-curvind_stats.csv
[command] - asegstats2table --meas volume --tablefile
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aseg_ses-study1_stat
s.csv --delimiter comma --subjects sub-02_run-38141
[info] - checking output:
/tmp/brainprep-sbm/derivatives/sbm/longitudinal/morphometry/aseg_ses-study1_stat
s.csv
[title] - Group Level SBM done.

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-sbm",
            "--t1_file", str(t1_file),
            "--output-dir", str(outdir),
            "--keep-intermediate",
        ] for subject_data in data.values()
          for t1_file in [subject_data.anat1, subject_data.anat2]
    ]
)
commands.append(
    [
        [
            "brainprep", "subject-level-sbm",
            "--t1_file", str(t1_file),
            "--output-dir", str(outdir),
            "--analysis-type", "nextbrain",
            "--keep-intermediate",
        ] for subject_data in data.values()
          for t1_file in [subject_data.anat1, subject_data.anat2]
    ]
)
commands.append(
    [
        [
            "brainprep", "longitudinal-sbm",
            "--t1_files",
            f"{subject_data.anat1},{subject_data.anat2}",
            "--output-dir", str(outdir),
            "--keep-intermediate",
        ] for subject_data in data.values()
    ]
)
commands.append(
    [
        [
            "brainprep", "group-level-sbm",
            "--output-dir", str(outdir),
            "--euler_threshold", "-217",
            "--keep-intermediate",
        ],
        [
            "brainprep", "group-level-sbm",
            "--output-dir", str(outdir),
            "--euler_threshold", "-217",
            "--longitudinal",
            "--keep-intermediate",
        ],
    ]
)
pprint(commands)

[[['brainprep',
   'subject-level-sbm',
   '--t1_file',
   '/tmp/brainprep-data/rawdata/sub-01/ses-study1/anat/sub-01_ses-study1_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--keep-intermediate'],
  ['brainprep',
   'subject-level-sbm',
   '--t1_file',
   '/tmp/brainprep-data/rawdata/sub-01/ses-study2/anat/sub-01_ses-study2_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--keep-intermediate'],
  ['brainprep',
   'subject-level-sbm',
   '--t1_file',
   '/tmp/brainprep-data/rawdata/sub-02/ses-study1/anat/sub-02_ses-study1_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--keep-intermediate'],
  ['brainprep',
   'subject-level-sbm',
   '--t1_file',
   '/tmp/brainprep-data/rawdata/sub-02/ses-study2/anat/sub-02_ses-study2_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--keep-intermediate']],
 [['brainprep',
   'subject-level-sbm',
   '--t1_file',
   '/tmp/brainprep-data/rawdata/sub-01/ses-study1/anat/sub-01_ses-study1_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--analysis-type',
   'nextbrain',
   '--keep-intermediate'],
  ['brainprep',
   'subject-level-sbm',
   '--t1_file',
   '/tmp/brainprep-data/rawdata/sub-01/ses-study2/anat/sub-01_ses-study2_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--analysis-type',
   'nextbrain',
   '--keep-intermediate'],
  ['brainprep',
   'subject-level-sbm',
   '--t1_file',
   '/tmp/brainprep-data/rawdata/sub-02/ses-study1/anat/sub-02_ses-study1_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--analysis-type',
   'nextbrain',
   '--keep-intermediate'],
  ['brainprep',
   'subject-level-sbm',
   '--t1_file',
   '/tmp/brainprep-data/rawdata/sub-02/ses-study2/anat/sub-02_ses-study2_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--analysis-type',
   'nextbrain',
   '--keep-intermediate']],
 [['brainprep',
   'longitudinal-sbm',
   '--t1_files',
   '/tmp/brainprep-data/rawdata/sub-01/ses-study1/anat/sub-01_ses-study1_T1w.nii.gz,/tmp/brainprep-data/rawdata/sub-01/ses-study2/anat/sub-01_ses-study2_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--keep-intermediate'],
  ['brainprep',
   'longitudinal-sbm',
   '--t1_files',
   '/tmp/brainprep-data/rawdata/sub-02/ses-study1/anat/sub-02_ses-study1_T1w.nii.gz,/tmp/brainprep-data/rawdata/sub-02/ses-study2/anat/sub-02_ses-study2_T1w.nii.gz',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--keep-intermediate']],
 [['brainprep',
   'group-level-sbm',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--euler_threshold',
   '-217',
   '--keep-intermediate'],
  ['brainprep',
   'group-level-sbm',
   '--output-dir',
   '/tmp/brainprep-sbm',
   '--euler_threshold',
   '-217',
   '--longitudinal',
   '--keep-intermediate']]]

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.

Total running time of the script: (0 minutes 2.841 seconds)

Estimated memory usage: 144 MB

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