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Fix for #17 #18

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Fix for #17 #18

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a31ffec
Fix for #17
celstark Apr 6, 2018
fbf3747
Fix sample call for #16
celstark Apr 6, 2018
c30f4ae
Added ability to control CPU count
celstark Feb 16, 2022
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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ docker pull bids/mindboggle
To run the docker, do:

```
docker run -ti -v $PWD/ds114_test1:/home/jovyan/work/data bids/mindboggle /home/jovyan/work/data /home/jovyan/work/data/derivatives/ participant
docker run -ti -v $PWD/ds114_test1:/home/jovyan/work/data bids/mindboggle /home/jovyan/work/data /home/jovyan/work/data participant
```

Its important to mount to a directory in `/home/jovyan/` because you are not root in this Docker image.
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23 changes: 13 additions & 10 deletions run.py
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Expand Up @@ -9,18 +9,20 @@
__version__ = open(os.path.join(os.path.dirname(os.path.realpath(__file__)), 'version')).read()

def get_t1_images(basedir, subject_label):
print(join(basedir,subject_label, "anat", "sub-%s_T1w.nii.gz" % (subject_label)))
print(join(basedir,subject_label, "anat", "sub-%s_ses-*_T1w.nii.gz" % (subject_label)))
out = glob(join(basedir,"sub-%s"%subject_label,"anat", "sub-%s_T1w.nii.gz" % (subject_label))) + \
glob(join(basedir,"sub-%s"%subject_label, "anat", "sub-%s_ses-*_T1w.nii.gz" % (subject_label)))
#print(join(basedir,subject_label, "anat", "sub-%s_run*_T1w.nii.gz" % (subject_label)))
#print(join(basedir,subject_label, "anat", "sub-%s_ses-*_T1w.nii.gz" % (subject_label)))
out = glob(join(basedir,"sub-%s"%subject_label,"anat", "sub-%s_*T1w.nii.gz" % (subject_label))) + \
glob(join(basedir,"sub-%s"%subject_label, "ses-*","anat", "sub-%s_ses-*_T1w.nii.gz" % (subject_label)))
return out

def run_mindboggle(image, subject_id, output_dir):
def run_mindboggle(image, subject_id, output_dir, ncpus):
#mindboggle123 $IMAGE --id $ID --out $OUT --working $WORKING
# "--plugin MultiProc --plugin_args dict(n_procs=2)"
cmd = ["mindboggle123", image,
"--id", subject_id,
"--out", join(output_dir, "derivatives", "mindboggle"),
"--working", join(output_dir,"scratch"),
"--working", join(output_dir,"scratch",subject_id),
"--fs_openmp",ncpus,"--ants_num_threads",ncpus,"--mb_num_threads",ncpus,
]
check_call(cmd)
return
Expand All @@ -46,6 +48,7 @@ def run_mindboggle(image, subject_id, output_dir):

parser.add_argument('-v', '--version', action='version',
version='BIDS-App Mindboggle version {}'.format(__version__))
parser.add_argument('-c', '--cpus', help='Number of CPU threads to use',nargs='?',default='1')

args = parser.parse_args()

Expand All @@ -58,8 +61,9 @@ def run_mindboggle(image, subject_id, output_dir):
subjects_to_analyze = [s.split("/")[-1].replace("sub-","") for s in glob(os.path.join(args.bids_dir, "sub*"))]

# running participant level
print(args)
print(subjects_to_analyze)
print("LOG: arguments: ",args)
print("LOG: subjects: ",subjects_to_analyze)
print("LOG: cpus: ",args.cpus)
if args.analysis_level == "participant":
print("running")
# find all T1s and skullstrip them
Expand All @@ -73,5 +77,4 @@ def run_mindboggle(image, subject_id, output_dir):
else:
label = "sub-%s" % subject_label

run_mindboggle(t1, label, args.output_dir)

run_mindboggle(t1, label, args.output_dir, args.cpus)