Merge pull request #21 from khanlab/lobefix

fix LOBE heuristic, move vNav files
khanlab · Aug 21, 2021 · 12e807d · 12e807d
2 parents dae0cc1 + 1bc7106
commit 12e807d
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Showing 2 changed files with 26 additions and 19 deletions.
diff --git a/etc/merge_vNav.py b/etc/merge_vNav.py
@@ -58,11 +58,17 @@ def zero_pad(m):
 
 
     #move all other files to sourcedata
-    print('moving vnav files to sourcedata, replacing with:')
+    print('moving vnav files to sourcedata/vNav, replacing with:')
     print(vnav_4d)
+
+    #create vNav folder in sourcedata:
+    from pathlib import Path
+    Path(os.path.join(bids_dir,'sourcedata','vNav')).mkdir(
+        parents=True, exist_ok=True)
+
     for f in glob.glob(prefix + 'vNav????.*'):
         (head,tail) = os.path.split(f)
-        os.rename(f,os.path.join(bids_dir,'sourcedata',tail))   
+        os.rename(f,os.path.join(bids_dir,'sourcedata','vNav',tail))   
 
     #save new 4d file
     nib_4d = nib.nifti1.Nifti1Image(vol_4d, init_nib.affine)

diff --git a/heuristics/LOBE_HCPLS.py b/heuristics/LOBE_HCPLS.py
@@ -77,24 +77,25 @@ def infotodict(seqinfo):
 
 
         # T1w images
-        if 'T1w_MPR_vNav_setter' in s.series_description:
-            if 'MOSAIC' in s.image_type:
-                info[t1w_vnavs].append({'item': s.series_id})
-
-        elif ('tfl_mgh_epinav_ABCD' in s.series_description):
-            if 'OTHER' in s.image_type: 
-                if 'NORM' in s.image_type:
-                    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:
-                    info[t1w_me_norm].append({'item': s.series_id})
+        if 'T1w_MPR' 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:
-                    info[t1w_me].append({'item': s.series_id})
-
-        elif ('T1w_MPR' in s.series_description):
-            info[t1w_basic].append({'item': s.series_id})
+                    if 'OTHER' in s.image_type: 
+                        if 'NORM' in s.image_type:
+                            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:
+                            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