fix: update heuristics to new style

Author: mgxd

heuristics/banda-bids.py

@@ -16,19 +16,19 @@ def infotodict(seqinfo):
     seqitem: run number during scanning
     subindex: sub index within group
     """
-    t1 = create_key('anat/sub-{subject}_T1w')
-    t2 = create_key('anat/sub-{subject}_T2w')
-    rest = create_key('func/sub-{subject}_task-rest_run-{item:02d}_bold')
-    rest_sbref = create_key('func/sub-{subject}_task-rest_run-{item:02d}_sbref')
-    face = create_key('func/sub-{subject}_task-face_run-{item:02d}_bold')
-    face_sbref = create_key('func/sub-{subject}_task-face_run-{item:02d}_sbref')
-    gamble = create_key('func/sub-{subject}_task-gambling_run-{item:02d}_bold')
-    gamble_sbref = create_key('func/sub-{subject}_task-gambling_run-{item:02d}_sbref')
-    conflict = create_key('func/sub-{subject}_task-conflict_run-{item:02d}_bold')
-    conflict_sbref = create_key('func/sub-{subject}_task-conflict_run-{item:02d}_sbref')
-    dwi = create_key('dwi/sub-{subject}_run-{item:02d}_dwi')
-    dwi_sbref = create_key('dwi/sub-{subject}_run-{item:02d}_sbref')
-    fmap = create_key('fmap/sub-{subject}_dir-{dir}_run-{item:02d}_epi')
+    t1 = create_key('sub-{subject}/anat/sub-{subject}_T1w')
+    t2 = create_key('sub-{subject}/anat/sub-{subject}_T2w')
+    rest = create_key('sub-{subject}/func/sub-{subject}_task-rest_run-{item:02d}_bold')
+    rest_sbref = create_key('sub-{subject}/func/sub-{subject}_task-rest_run-{item:02d}_sbref')
+    face = create_key('sub-{subject}/func/sub-{subject}_task-face_run-{item:02d}_bold')
+    face_sbref = create_key('sub-{subject}/func/sub-{subject}_task-face_run-{item:02d}_sbref')
+    gamble = create_key('sub-{subject}/func/sub-{subject}_task-gambling_run-{item:02d}_bold')
+    gamble_sbref = create_key('sub-{subject}/func/sub-{subject}_task-gambling_run-{item:02d}_sbref')
+    conflict = create_key('sub-{subject}/func/sub-{subject}_task-conflict_run-{item:02d}_bold')
+    conflict_sbref = create_key('sub-{subject}/func/sub-{subject}_task-conflict_run-{item:02d}_sbref')
+    dwi = create_key('sub-{subject}/dwi/sub-{subject}_run-{item:02d}_dwi')
+    dwi_sbref = create_key('sub-{subject}/dwi/sub-{subject}_run-{item:02d}_sbref')
+    fmap = create_key('sub-{subject}/fmap/sub-{subject}_dir-{dir}_run-{item:02d}_epi')
 
     info = {t1:[], t2:[],
             rest:[], face:[], gamble:[], conflict:[], dwi:[],

heuristics/bids_with_ses.py

@@ -18,22 +18,21 @@ def infotodict(seqinfo):
     subindex: sub index within group
     session: scan index for longitudinal acq
     """
-    and_dicom = ('dicom', 'nii.gz')
+    # for this example, we want to include copies of the DICOMs just for our T1
+    # and functional scans
+    outdicom = ('dicom', 'nii.gz')
 
-    t1 = create_key('{session}/anat/sub-{subject}_T1w', outtype=and_dicom)
-    t2 = create_key('{session}/anat/sub-{subject}_T2w', outtype=and_dicom)
-    fm_diff = create_key('{session}/fmap/sub-{subject}_fieldmap-dwi')
-    dwi_ap = create_key('{session}/dwi/sub-{subject}_dir-AP_dwi', outtype=and_dicom)
-    dwi_pa = create_key('{session}/dwi/sub-{subject}_dir-PA_dwi', outtype=and_dicom)
-    fm_rest= create_key('{session}/fmap/sub-{subject}_fieldmap-rest')
-    rs = create_key('{session}/func/sub-{subject}_task-rest_run-{item:02d}_bold', outtype=and_dicom)
-    boldt1 = create_key('{session}/func/sub-{subject}_task-bird1back_run-{item:02d}_bold', outtype=and_dicom)
-    boldt2 = create_key('{session}/func/sub-{subject}_task-letter1back_run-{item:02d}_bold', outtype=and_dicom)
-    boldt3 = create_key('{session}/func/sub-{subject}_task-letter2back_run-{item:02d}_bold', outtype=and_dicom)
-    nofb_task=create_key('{session}/func/sub-{subject}_task-nofb_run-{item:02d}_bold', outtype=and_dicom)
-    fb_task=create_key('{session}/func/sub-{subject}_task-fb_run-{item:02d}_bold', outtype=and_dicom)
-    info = {t1: [], t2:[], fm_diff:[], dwi_ap:[], dwi_pa:[], fm_rest:[], rs:[],
-            boldt1:[], boldt2:[], boldt3:[], nofb_task:[], fb_task:[]}
+    t1 = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_T1w', outtype=outdicom)
+    t2 = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_T2w')
+    dwi_ap = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_dir-AP_dwi')
+    dwi_pa = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_dir-PA_dwi')
+    rs = create_key('{bids_subject_session_dir}/func/{bids_subject_session_prefix}_task-rest_run-{item:02d}_bold', outtype=outdicom)
+    boldt1 = create_key('{bids_subject_session_dir}/func/{bids_subject_session_prefix}_task-bird1back_run-{item:02d}_bold', outtype=outdicom)
+    boldt2 = create_key('{bids_subject_session_dir}/func/{bids_subject_session_prefix}_task-letter1back_run-{item:02d}_bold', outtype=outdicom)
+    boldt3 = create_key('{bids_subject_session_dir}/func/{bids_subject_session_prefix}_task-letter2back_run-{item:02d}_bold', outtype=outdicom)
+
+    info = {t1: [], t2:[], dwi_ap:[], dwi_pa:[], rs:[],
+            boldt1:[], boldt2:[], boldt3:[],}
     last_run = len(seqinfo)
     for s in seqinfo:
         if (s.dim3 == 176 or s.dim3 == 352) and (s.dim4 == 1) and ('MEMPRAGE' in s.protocol_name):
@@ -42,14 +41,10 @@ def infotodict(seqinfo):
             info[t1] = [s.series_id]
         elif (s.dim3 == 176 or s.dim3 == 352) and (s.dim4 == 1) and ('T2_SPACE' in s.protocol_name):
             info[t2] = [s.series_id]
-        elif ('field_mapping_diffusion' in s.protocol_name):
-            info[fm_diff].append([s.series_id])
         elif (s.dim4 >= 70) and ('DIFFUSION_HighRes_AP' in s.protocol_name):
             info[dwi_ap].append([s.series_id])
         elif ('DIFFUSION_HighRes_PA' in s.protocol_name):
             info[dwi_pa].append([s.series_id])
-        elif ('field_mapping_resting' in s.protocol_name):
-            info[fm_rest].append([s.series_id])
         elif (s.dim4 == 144) and ('resting' in s.protocol_name):
             if not s.is_motion_corrected:
                 info[rs].append([(s.series_id)])
@@ -62,13 +57,4 @@ def infotodict(seqinfo):
         elif (s.dim4 == 227 or s.dim4 == 454) and ('transfer2' in s.protocol_name):
             if not s.is_motion_corrected:
                 info[boldt3].append([s.series_id])
-        elif (('run1' in s.protocol_name) or ('run6' in s.protocol_name)) and (s.dim4 == 159):
-            if not s.is_motion_corrected:
-               info[nofb_task].append([s.series_id])
-        elif (('run2' in s.protocol_name) or ('run3' in s.protocol_name) or ('run4' in s.protocol_name)
-                or ('run5' in s.protocol_name)) and (s.dim4 == 159):
-            if not s.is_motion_corrected:
-                info[fb_task].append([s.series_id])
-        else:
-            pass
     return info