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@@ -47,35 +47,32 @@ warnings.filterwarnings("ignore", message="numpy.ufunc size changed*")
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job_template = """
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#PBS -l walltime=5:00:00
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#PBS -j oe
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-#PBS -o /home/mpib/wittkuhn/highspeed/logs/masks
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+#PBS -o /home/mpib/wittkuhn/highspeed/highspeed-masks/logs
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#PBS -m n
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#PBS -v FSLOUTPUTTYPE=NIFTI_GZ
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source /etc/bash_completion.d/virtualenvwrapper
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-workon glm
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+workon highspeed-masks
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module load fsl/5.0
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module load freesurfer/6.0.0
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"""
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# ======================================================================
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# DEFINE PATHS AND SUBJECTS
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# ======================================================================
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-# define paths depending on the operating system (OS) platform:
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path_root = None
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sub_list = None
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-if 'darwin' in sys.platform:
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- path_root = opj('/Users', 'wittkuhn', 'Volumes', 'tardis', 'highspeed')
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- sub_list = ['sub-01']
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-elif 'linux' in sys.platform:
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- path_root = opj('/home', 'mpib', 'wittkuhn', 'highspeed')
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- # grab the list of subjects from the bids data set:
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- layout = BIDSLayout(opj(path_root, 'bids'))
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- # get all subject ids:
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- sub_list = sorted(layout.get_subjects())
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- # create a template to add the "sub-" prefix to the ids
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- sub_template = ['sub-'] * len(sub_list)
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- # add the prefix to all ids:
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- sub_list = ["%s%s" % t for t in zip(sub_template, sub_list)]
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- # if user defined to run specific subject
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- sub_list = sub_list[int(sys.argv[1]):int(sys.argv[2])]
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+# path to the project root:
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+project_name = 'highspeed-masks'
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+path_root = os.getcwd().split(project_name)[0] + project_name
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+# grab the list of subjects from the bids data set:
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+layout = BIDSLayout(opj(path_root, 'bids'))
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+# get all subject ids:
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+sub_list = sorted(layout.get_subjects())
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+# create a template to add the "sub-" prefix to the ids
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+sub_template = ['sub-'] * len(sub_list)
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+# add the prefix to all ids:
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+sub_list = ["%s%s" % t for t in zip(sub_template, sub_list)]
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+# if user defined to run specific subject
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+sub_list = sub_list[int(sys.argv[1]):int(sys.argv[2])]
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# ======================================================================
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# DEFINE NODE: INFOSOURCE
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# ======================================================================
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@@ -89,11 +86,11 @@ infosource.iterables = [('subject_id', sub_list)]
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# ======================================================================
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# define all relevant files paths:
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templates = dict(
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- func=opj(path_root, 'derivatives', 'fmriprep', '{subject_id}', '*',
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+ func=opj(path_root, 'fmriprep', '{subject_id}', '*',
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'func', '*space-T1w*preproc_bold.nii.gz'),
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- func_parc=opj(path_root, 'derivatives', 'fmriprep', '{subject_id}',
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+ func_parc=opj(path_root, 'fmriprep', '{subject_id}',
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'*', 'func', '*space-T1w*aparcaseg_dseg.nii.gz'),
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- wholemask=opj(path_root, 'derivatives', 'fmriprep', '{subject_id}',
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+ wholemask=opj(path_root, 'fmriprep', '{subject_id}',
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'*', 'func', '*space-T1w*brain_mask.nii.gz'),
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)
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# define the selectfiles node:
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