openfmri pieces

00_reconfigure existing layouts.sh

#!/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

01_simple_heuristic.py

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

03_complex_heuristic.py

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