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openfmri pieces
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| #!/bin/bash | |
| for sub in '315' '318' '332' ; do | |
| for run in 1 2 3 4 ; do | |
| mkdir /om/project/gates/wmfilt/openfmri/ds001/${sub} | |
| mkdir /om/project/gates/wmfilt/openfmri/ds001/${sub}/model | |
| mkdir /om/project/gates/wmfilt/openfmri/ds001/${sub}/model/model001 | |
| mkdir /om/project/gates/wmfilt/openfmri/ds001/${sub}/model/model001/onsets | |
| mkdir /om/project/gates/wmfilt/openfmri/ds001/${sub}/model/model001/onsets/task001_run00${run} | |
| mkdir /om/project/gates/wmfilt/openfmri/ds001/${sub}/BOLD | |
| mkdir /om/project/gates/wmfilt/openfmri/ds001/${sub}/BOLD/task001_run00${run} | |
| mkdir /om/project/gates/wmfilt/openfmri/ds001/${sub}/behav | |
| mkdir /om/project/gates/wmfilt/openfmri/ds001/${sub}/anatomy | |
| #T1 | |
| ln -s /mindhive/xnat/data/GATES/${sub}/niftis/mprag2.nii /om/project/gates/wmfilt/openfmri/ds001/${sub}/anatomy/T1.nii | |
| #BOLD | |
| ln -s /mindhive/xnat/data/GATES/${sub}/niftis/WM${run}.nii /om/project/gates/wmfilt/openfmri/ds001/${sub}/BOLD/task001_run00${run}/bold.nii | |
| ln -s /om/project/gates/wmfilt/openfmri/scan_key.txt /om/project/gates/wmfilt/openfmri/ds001/${sub}/BOLD/task001_run00${run}/scan_key.txt | |
| #model | |
| ln -s /om/project/gates/wmfilt/bips/onsets/wmfilt_run${run}/${sub}_delay_2R_c.txt /om/project/gates/wmfilt/openfmri/ds001/${sub}/model/model001/onsets/task001_run00${run}/cond001.txt | |
| ln -s /om/project/gates/wmfilt/bips/onsets/wmfilt_run${run}/${sub}_delay_2R_m.txt /om/project/gates/wmfilt/openfmri/ds001/${sub}/model/model001/onsets/task001_run00${run}/cond002.txt | |
| ln -s /om/project/gates/wmfilt/bips/onsets/wmfilt_run${run}/${sub}_delay_4RY_c.txt /om/project/gates/wmfilt/openfmri/ds001/${sub}/model/model001/onsets/task001_run00${run}/cond003.txt | |
| ln -s /om/project/gates/wmfilt/bips/onsets/wmfilt_run${run}/${sub}_delay_4RY_m.txt /om/project/gates/wmfilt/openfmri/ds001/${sub}/model/model001/onsets/task001_run00${run}/cond004.txt | |
| ln -s /om/project/gates/wmfilt/bips/onsets/wmfilt_run${run}/${sub}_delay_DRY_c.txt /om/project/gates/wmfilt/openfmri/ds001/ | |
| done | |
| done |
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| import os | |
| def create_key(template, outtype=('nii.gz',), annotation_classes=None): | |
| if template is None or not template: | |
| raise ValueError('Template must be a valid format string') | |
| return (template, outtype, annotation_classes) | |
| def infotodict(seqinfo): | |
| """Heuristic evaluator for determining which runs belong where | |
| allowed template fields - follow python string module: | |
| item: index within category | |
| subject: participant id | |
| seqitem: run number during scanning | |
| subindex: sub index within group | |
| """ | |
| # Create the T1 anatomy file | |
| t1 = create_key('anatomy/T1_{item:03d}') | |
| # Pull out the non word reptition fMRI run | |
| nwr = create_key('BOLD/task001_run{item:03d}/bold') | |
| #initialize a dictionary for all the scans you'll be grabbing | |
| info = {t1:[],nwr:[]} | |
| # commented out because not needed anymore | |
| #info={} | |
| # the basic "if" statement structure is a hack job customized to every project | |
| # the first part of the if condition filters by some "unique-ish" number from columns 6,7,8, and 9 | |
| # the second, and, part of the condition filters by hopefully a meaningful sequence name that was used in the scanner. | |
| # Note: the t1 image is NOT appended to info. Keep only the very last t1 run in the file. | |
| # Note: the functional sequences use .append when adding values to the dictionary key. This is because multiple runs will have the same MRI sequence name, but we want all of them. | |
| # Note: The 13th column is a boolean that refers to motion correction. Only keep runs where the boolean is false. | |
| last_run = len(seqinfo) | |
| for s in seqinfo: | |
| x,y,sl,nt = (s[6], s[7], s[8], s[9]) | |
| if (sl == 176) and (nt ==1) and ('T1_MPRAGE' in s[12]): | |
| info[t1]=[s[2]] | |
| elif (nt == 42) and ('Nonword-Repetition' in s[12]): | |
| if not s[13]: | |
| info[nwr].append(s[2]) | |
| else: | |
| pass | |
| return info |
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| import os | |
| def create_key(template, outtype=('nii.gz',), annotation_classes=None): | |
| if template is None or not template: | |
| raise ValueError('Template must be a valid format string') | |
| return (template, outtype, annotation_classes) | |
| def infotodict(seqinfo): | |
| """Heuristic evaluator for determining which runs belong where | |
| allowed template fields - follow python string module: | |
| item: index within category | |
| subject: participant id | |
| seqitem: run number during scanning | |
| subindex: sub index within group | |
| """ | |
| rs = create_key('resting/rest/bold', outtype=('dicom', 'nii.gz')) | |
| spin = create_key('resting/rest/se', outtype=('dicom', 'nii.gz')) | |
| dwi = create_key('dmri/dwi_{item:03d}', outtype=('dicom',)) | |
| t1 = create_key('anatomy/T1_{item:03d}') | |
| t2 = create_key('anatomy/T2_{item:03d}') | |
| pataka = create_key('BOLD/task001_run{item:03d}/bold') | |
| sentences=create_key('BOLD/task002_run{item:03d}/bold') | |
| nonwordrep=create_key('BOLD/task003_run{item:03d}/bold') | |
| facematch=create_key('BOLD/task004_run{item:03d}/bold') | |
| emosent=create_key('BOLD/task005_run{item:03d}/bold') | |
| vowels=create_key('BOLD/task006_run{item:03d}/bold') | |
| pitch_emph=create_key('BOLD/task007_run{item:03d}/bold') | |
| movie_trailer=create_key('BOLD/task008_run{item:03d}/bold') | |
| info = {rs: [], spin: [], dwi:[], t1:[], t2:[], pataka:[], sentences:[], nonwordrep:[], facematch:[], emosent:[], vowels:[], pitch_emph:[], movie_trailer:[]} | |
| last_run = len(seqinfo) | |
| for s in seqinfo: | |
| x,y,sl,nt = (s[6], s[7], s[8], s[9]) | |
| if (nt == 300) and ('SMS5_rsfMRI' in s[12]): | |
| info[rs] = [s[2]] | |
| elif (nt == 4) and ('Spin_Echo' in s[12]): | |
| info[spin].append(s[2]) | |
| elif (sl > 1) and (nt == 72) and ('SMS2-diff_b1000' in s[12]): | |
| info[dwi].append(s[2]) | |
| elif (sl > 1) and (nt == 7 ) and ('SMS2-diff_b100_free' in s[12]): | |
| info[dwi].append(s[2]) | |
| elif (sl == 176) and (nt ==1) and ('T1_MPRAGE' in s[12]): | |
| info[t1].append(s[2]) | |
| elif (nt > 175) and ('PaTaKa' in s[12]): | |
| info[pataka].append(s[2]) | |
| elif (nt == 57) and ('Sentences' in s[12]): | |
| info[sentences].append(s[2]) | |
| elif (nt == 42 ) and ('Nonword' in s[12]): | |
| info[nonwordrep].append(s[2]) | |
| elif (nt == 99) and ('FaceMatch' in s[12]): | |
| info[facematch].append(s[2]) | |
| elif (nt == 42) and ('EmoSent' in s[12]): | |
| info[emosent].append(s[2]) | |
| elif (nt == 55) and ('Vowels' in s[12]): | |
| info[vowels].append(s[2]) | |
| elif (nt == 101) and ('PitchEmph' in s[12]): | |
| info[pitch_emph].append(s[2]) | |
| elif (nt == 138) and ('Movie' in s[12]): | |
| info[movie_trailer].append(s[2]) | |
| elif (sl == 176) and (nt == 1 ) and ('T2_SPACE' in s[12]): | |
| info[t2] = [s[2]] | |
| else: | |
| pass | |
| return info |
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