Add correctFieldMapCase4 to support pepolar fieldmaps #39
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,29 @@ | ||
| #!/bin/bash | ||
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| if [ "$#" -lt 1 ] | ||
| then | ||
| echo "Usage: $0 <in_bids> <subj ID> <session id (optional)>" | ||
| exit 1 | ||
| fi | ||
| in_bids=$1 | ||
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| exec_path=`dirname $0` | ||
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| subj=$2 | ||
| subj=${subj##sub-} #strip off sub- if it exists, to make consistent | ||
| if [ "$#" -gt 2 ] | ||
| then | ||
| ses=$3 | ||
| ses=${ses##ses-} #strip off sub- if it exists, to make consistent | ||
| fi | ||
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| #correct field map json files | ||
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| if [ -n "$ses" ] | ||
| then | ||
| $exec_path/correctFieldMapJsonCase4.py $in_bids sub-$subj ses-$ses | ||
| else | ||
| $exec_path/correctFieldMapJsonCase4.py $in_bids sub-$subj | ||
| fi | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| #! /usr/bin/env python3 | ||
| ''' | ||
| correct field map json | ||
| ''' | ||
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| import os | ||
| import sys | ||
| import json | ||
| import glob | ||
| import collections | ||
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| def correctFieldMapJson(bids_dir,sub,ses=None): | ||
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| if ses: #ses not None | ||
| sub_prefix = '{}_{}'.format(sub,ses) | ||
| sub_path_prefix=os.path.join(sub,ses) | ||
| sub_root = '{}'.format(sub) | ||
| else: | ||
| sub_prefix = '{}'.format(sub) | ||
| sub_path_prefix = sub_prefix | ||
| sub_root = '{}'.format(sub) | ||
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| sub_dir=os.path.join(bids_dir,sub_path_prefix) | ||
| sub_root_dir=os.path.join(bids_dir,sub_root) #without session | ||
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| for fmri_json_file in glob.glob(os.path.join(sub_dir,'fmap','{}_acq-EPI_dir-*_epi.json'.format(sub_prefix))): | ||
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| #debug | ||
| print(fmri_json_file) | ||
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| #load json files | ||
| with open(fmri_json_file, 'r') as f: | ||
| fmri_json = json.load(f,object_pairs_hook=collections.OrderedDict) | ||
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| # apply to all bold images | ||
| cwd=os.getcwd() | ||
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There was a problem hiding this comment. I guess we're changing the working directory to get the paths relative to the participant directory? I try to avoid changing directories if possible (can cause problems e.g. if the script fails or is cancelled part way through) but if this is the easiest way to do it, that's fine. |
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| os.chdir(sub_root_dir) | ||
| if ses: | ||
| all_bold = glob.glob(os.path.join('{}'.format(ses),'func','{}_*_bold.nii.gz'.format(sub_prefix))) | ||
| else: | ||
| all_bold = glob.glob(os.path.join('func','{}_*_bold.nii.gz'.format(sub_prefix))) | ||
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| os.chdir(cwd) | ||
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| fmri_json["IntendedFor"]=all_bold | ||
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| #update json file | ||
| os.system("chmod a+w {}".format(fmri_json_file)) | ||
| with open(fmri_json_file, 'w') as f: | ||
| json.dump(fmri_json, f, indent=4, separators=(',', ': ')) | ||
| os.system("chmod a-w {}".format(fmri_json_file)) | ||
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| if __name__=="__main__": | ||
| if len(sys.argv)-1 < 2: | ||
| print ("Usage: python " + os.path.basename(__file__)+ " 'bids_dir' 'sub' 'ses (optional)'") | ||
| sys.exit() | ||
| else: | ||
| bids_dir = sys.argv[1] | ||
| sub = sys.argv[2] | ||
| if len(sys.argv)-1 > 2: | ||
| ses=sys.argv[3] | ||
| correctFieldMapJson(bids_dir,sub,ses) | ||
| else: | ||
| correctFieldMapJson(bids_dir,sub) | ||
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| #test | ||
| #Usage: python correctFieldMapJson.py 'bids_dir' 'sub' | ||
| #python correctFieldMapJson.py '/mnt/hgfs/test/correct_fieldmap_json/topsy_7T' 'sub-005' | ||
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I think this can just be
sub_root = sub(or maybesub_root = str(sub)ifsubmight not already be a string).Actually, you may just want to get rid of this variable entirely because it seems to be the same as
subin all cases.