Create cfmm_vnav.py

heuristics/cfmm_vnav.py

@@ -0,0 +1,175 @@
+import os
+
+# Adaptation of HCP-Lifespan & LOBE protocol 
+# Requires tar2bids > v0.0.5h for vNav clean-up
+
+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
+    """
+
+    t1w = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-MPRvNav4eRMS_run-{item}_T1w')
+    t1w_me = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-MPRvNav4e_run-{item}_echo_MEMPRAGE')
+    t1w_norm = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-MPRvNavNorm4eRMS_run-{item}_T1w')
+    t1w_me_norm = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-MPRvNavNorm4e_run-{item}_echo_MEMPRAGE')
+    t1w_vnavs = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-MPRvNav_run-{item}_vNav')
+
+    t2w = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-SPCvNavRMS_run-{item}_T2w')
+    t2w_norm = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-SPCvNavNormRMS_run-{item}_T2w')
+    t2w_vnavs = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-SPCvNav_run-{item}_vNav')
+
+
+    t1w_basic = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-MPRAGE_run-{item}_T1w')
+    t2w_basic = create_key('{bids_subject_session_dir}/anat/{bids_subject_session_prefix}_acq-SPACE_run-{item}_T2w')
+
+    #Diffusion
+    dwi_ap = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_dir-AP_run-{item}_dwi')
+    dwi_ap_sbref = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_dir-AP_run-{item}_sbref')
+    dwi_pa = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_dir-PA_run-{item}_dwi')
+    dwi_pa_sbref = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_dir-PA_run-{item}_sbref')
+    dwi_lr = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_dir-LR_run-{item}_dwi')
+    dwi_lr_sbref = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_dir-LR_run-{item}_sbref')
+    dwi_rl = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_dir-RL_run-{item}_dwi')
+    dwi_rl_sbref = create_key('{bids_subject_session_dir}/dwi/{bids_subject_session_prefix}_dir-RL_run-{item}_sbref')
+
+
+
+    #Field Maps:
+    fmap_spinecho_ap = create_key('{bids_subject_session_dir}/fmap/{bids_subject_session_prefix}_acq-spinecho_dir-AP_run-{item}_epi')
+    fmap_spinecho_pa = create_key('{bids_subject_session_dir}/fmap/{bids_subject_session_prefix}_acq-spinecho_dir-PA_run-{item}_epi')
+
+    movie_ap = create_key('{bids_subject_session_dir}/func/{bids_subject_session_prefix}_task-movie_acq-AP_run-{item}_bold')
+    movie_ap_sbref = create_key('{bids_subject_session_dir}/func/{bids_subject_session_prefix}_task-movie_acq-AP_run-{item}_sbref')
+
+    movie_pa = create_key('{bids_subject_session_dir}/func/{bids_subject_session_prefix}_task-movie_acq-PA_run-{item}_bold')
+    movie_pa_sbref = create_key('{bids_subject_session_dir}/func/{bids_subject_session_prefix}_task-movie_acq-PA_run-{item}_sbref')
+
+    rest_ap = create_key('{bids_subject_session_dir}/func/{bids_subject_session_prefix}_task-rest_acq-AP_run-{item}_bold')
+    rest_ap_sbref = create_key('{bids_subject_session_dir}/func/{bids_subject_session_prefix}_task-rest_acq-AP_run-{item}_sbref')
+    rest_pa = create_key('{bids_subject_session_dir}/func/{bids_subject_session_prefix}_task-rest_acq-PA_run-{item}_bold')
+    rest_pa_sbref = create_key('{bids_subject_session_dir}/func/{bids_subject_session_prefix}_task-rest_acq-PA_run-{item}_sbref')
+
+
+
+    info = {t1w_me:[],t1w_me_norm:[],t1w_vnavs:[],t1w:[],t1w_norm:[],
+         t2w_vnavs:[],t2w:[],t2w_norm:[],
+         t1w_basic:[],t2w_basic:[],
+         rest_ap:[],rest_ap_sbref:[],
+         rest_pa:[],rest_pa_sbref:[],
+         movie_ap:[],movie_ap_sbref:[],
+         movie_pa:[],movie_pa_sbref:[],
+         dwi_ap:[],dwi_pa:[],dwi_ap_sbref:[],dwi_pa_sbref:[],
+         dwi_lr:[],dwi_rl:[],dwi_lr_sbref:[],dwi_rl_sbref:[],
+         fmap_spinecho_ap:[],fmap_spinecho_pa:[]}
+
+    for idx, s in enumerate(seqinfo):
+
+
+        # T1w images
+        if 'T1w' in s.series_description:
+            if 'vNav' in s.series_description:
+                if 'setter' in s.series_description:
+                    if 'MOSAIC' in s.image_type:
+                        info[t1w_vnavs].append({'item': s.series_id})
+                else:
+                    if 'OTHER' in s.image_type: 
+                        if 'NORM' in s.image_type:
+                            print('skipping pre-scan norm RMS combined T1w')
+                            #info[t1w_norm].append({'item': s.series_id})
+                        else:
+                            info[t1w].append({'item': s.series_id})
+                    if 'M' in s.image_type: 
+                        if 'NORM' in s.image_type:
+                            print('skipping pre-scan norm separated echo T1w')
+                            #info[t1w_me_norm].append({'item': s.series_id})
+                        else:
+                            info[t1w_me].append({'item': s.series_id})
+
+            else:
+                info[t1w_basic].append({'item': s.series_id})
+
+
+        #T2w images
+        if 'T2w' in s.series_description:
+            if 'setter' in s.series_description:
+                if 'MOSAIC' in s.image_type:
+                    info[t2w_vnavs].append({'item': s.series_id})
+            elif 'vNav' in s.series_description:
+                if 'NORM' in s.image_type:
+                    print('skipping pre-scan norm T2w')
+#                    info[t2w_norm].append({'item': s.series_id}) 
+                else:
+                    info[t2w].append({'item': s.series_id}) 
+            else:
+                info[t2w_basic].append({'item': s.series_id})
+
+        #spinecho field maps
+
+        if ('SpinEchoFieldMap_AP' in s.series_description):   
+            info[fmap_spinecho_ap].append({'item': s.series_id})
+
+        if ('SpinEchoFieldMap_PA' in s.series_description):   
+            info[fmap_spinecho_pa].append({'item': s.series_id})
+
+
+        #dwi
+        if 'dMRI' in s.series_description or 'diff' in s.series_description:
+            if 'AP' in s.series_description:
+                if 'DIFFUSION' in s.image_type and 'ORIGINAL' in s.image_type:
+                    info[dwi_ap].append({'item': s.series_id})
+                elif 'SBRef' in s.series_description:
+                    info[dwi_ap_sbref].append({'item': s.series_id})
+            if 'PA' in s.series_description:
+                if 'DIFFUSION' in s.image_type and 'ORIGINAL' in s.image_type:
+                    info[dwi_pa].append({'item': s.series_id})
+                elif 'SBRef' in s.series_description:
+                    info[dwi_pa_sbref].append({'item': s.series_id})
+            if 'LR' in s.series_description:
+                if 'DIFFUSION' in s.image_type and 'ORIGINAL' in s.image_type:
+                    info[dwi_lr].append({'item': s.series_id})
+                elif 'SBRef' in s.series_description:
+                    info[dwi_lr_sbref].append({'item': s.series_id})
+            if 'RL' in s.series_description:
+                if 'DIFFUSION' in s.image_type and 'ORIGINAL' in s.image_type:
+                    info[dwi_rl].append({'item': s.series_id})
+                elif 'SBRef' in s.series_description:
+                    info[dwi_rl_sbref].append({'item': s.series_id})
+
+
+        #rs func (incl opp phase enc)
+        if 'rfMRI_REST_AP' in s.series_description:
+            if (s.dim4==1 and 'SBRef' in s.series_description):
+                info[rest_ap_sbref].append({'item': s.series_id})
+            else:
+                info[rest_ap].append({'item': s.series_id})
+        if 'rfMRI_REST_PA' in s.series_description:
+            if (s.dim4==1 and 'SBRef' in s.series_description):
+                info[rest_pa_sbref].append({'item': s.series_id})
+            else:
+                info[rest_pa].append({'item': s.series_id})
+
+        if 'movie_AP' in s.series_description:
+            if (s.dim4==1 and 'SBRef' in s.series_description):
+                info[movie_ap_sbref].append({'item': s.series_id})
+            else:
+                info[movie_ap].append({'item': s.series_id})
+
+        if 'movie_PA' in s.series_description:
+            if (s.dim4==1 and 'SBRef' in s.series_description):
+                info[movie_pa_sbref].append({'item': s.series_id})
+            else:
+                info[movie_pa].append({'item': s.series_id})
+
+
+    return info