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@mgxd
Created August 2, 2018 19:37
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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
"""
# anatomical
t1 = create_key('sub-{subject}/anat/sub-{subject}_acq-vNav_T1w')
t2 = create_key('sub-{subject}/anat/sub-{subject}_acq-vNav_T2w')
# field map (epi)
fmap_ap = create_key('sub-{subject}/fmap/sub-{subject}_dir-AP_run-{item:01d}_epi')
fmap_pa = create_key('sub-{subject}/fmap/sub-{subject}_dir-PA_run-{item:01d}_epi')
# BOLD
rest = create_key('sub-{subject}/func/sub-{subject}_task-rest_run-{item:01d}_bold')
dynloc = create_key('sub-{subject}/func/sub-{subject}_task-dynloc_run-{item:01d}_bold')
langloc = create_key('sub-{subject}/func/sub-{subject}_task-langloc_run-{item:01d}_bold')
wmspatial = create_key('sub-{subject}/func/sub-{subject}_task-wmspatial_run-{item:01d}_bold')
sart = create_key('sub-{subject}/func/sub-{subject}_task-sart_run-{item:01d}_bold')
# dwi
dwi98 = create_key('sub-{subject}/dwi/sub-{subject}_acq-dir98_run-{item:01d}_dwi')
dwi99 = create_key('sub-{subject}/dwi/sub-{subject}_acq-dir99_run-{item:01d}_dwi')
# sbref
dwi98sb = create_key('sub-{subject}/dwi/sub-{subject}_acq-dir98_run-{item:01d}_sbref')
dwi99sb = create_key('sub-{subject}/dwi/sub-{subject}_acq-dir99_run-{item:01d}_sbref')
restsb = create_key('sub-{subject}/func/sub-{subject}_task-rest_run-{item:01d}_sbref')
dynlocsb = create_key('sub-{subject}/func/sub-{subject}_task-dynloc_run-{item:01d}_sbref')
langlocsb = create_key('sub-{subject}/func/sub-{subject}_task-langloc_run-{item:01d}_sbref')
wmspatialsb = create_key('sub-{subject}/func/sub-{subject}_task-wmspatial_run-{item:01d}_sbref')
sartsb = create_key('sub-{subject}/func/sub-{subject}_task-sart_run-{item:01d}_sbref')
info = {t1: [], t2: [], # anatomical
fmap_ap: [], fmap_pa: [], # field maps
dwi98: [], dwi99: [], # diffusion
rest: [], dynloc: [], langloc: [], wmspatial: [], sart: [], # BOLD
dwi98sb: [], dwi99sb: [], restsb: [], dynlocsb: [],
langlocsb: [], wmspatialsb: [], sartsb: [], #SB reference
}
for idx, s in enumerate(seqinfo):
# helper definitions
is_sbref = 'SBRef' in s.series_description
# T1
if (s.dim3 == 208) and (s.dim4 == 1):
if 'T1w' in s.protocol_name:
info[t1] = [s.series_id]
elif 'T2w' in s.protocol_name:
info[t2] = [s.series_id]
# field maps
elif (s.dim3 == 72) and (s.dim4 == 3) and ('fmap-epi' in s.protocol_name):
if 'dir-AP' in s.protocol_name:
info[fmap_ap].append(s.series_id)
elif 'dir-PA' in s.protocol_name:
info[fmap_pa].append(s.series_id)
# diffusion
elif 'dwi' in s.protocol_name:
if 'dir98' in s.protocol_name:
if s.dim4 == 99:
info[dwi98].append(s.series_id)
elif is_sbref:
info[dwi98sb].append(s.series_id)
elif 'dir99' in s.protocol_name:
if s.dim4 == 100:
info[dwi99].append(s.series_id)
elif is_sbref:
info[dwi99sb].append(s.series_id)
elif 'func-bold' in s.protocol_name:
if 'task-rest' in s.protocol_name:
if s.dim4 >= 400:
info[rest].append(s.series_id)
elif is_sbref:
info[restsb].append(s.series_id)
elif 'task-dynloc' in s.protocol_name:
if s.dim4 >= 280:
info[dynloc].append(s.series_id)
elif is_sbref:
info[dynlocsb].append(s.series_id)
elif 'task-langloc' in s.protocol_name:
if s.dim4 >= 465:
info[langloc].append(s.series_id)
elif is_sbref:
info[langlocsb].append(s.series_id)
elif 'task-wmspatial' in s.protocol_name:
if s.dim4 >= 500:
info[wmspatial].append(s.series_id)
elif is_sbref:
info[wmspatialsb].append(s.series_id)
elif 'task-sart' in s.protocol_name:
if s.dim4 >= 400:
info[sart].append(s.series_id)
elif is_sbref:
info[sartsb].append(s.series_id)
return info
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