fix for pd+t2 naming scheme, and parsing

khanlab · Oct 15, 2020 · 1d5f697 · 1d5f697
1 parent a499563
commit 1d5f697
Show file tree

Hide file tree

Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/etc/pdt2_bids_corrector.py b/etc/pdt2_bids_corrector.py
@@ -29,12 +29,12 @@
     #in the case of echo-1, the EchoNumber tag does not exist in the json file    
     if ("EchoNumber" not in data) and ("_echo_" in i):
         js_addEchoNum = re.sub("_echo_", "_echo-1_", i)
-        js_changeEnding = re.sub("PDT2.*", "PDT2.json", js_addEchoNum)
+        js_changeEnding = re.sub("_PDT2[0-9]+.*", "_PDT2.json", js_addEchoNum)
         print('renaming: '+i+' to '+js_changeEnding)
         os.rename(i, js_changeEnding)
 
         ni_addEchoNum = re.sub("_echo_", "_echo-1_", k)
-        ni_changeEnding = re.sub("PDT2.*", "PDT2.nii.gz", ni_addEchoNum)
+        ni_changeEnding = re.sub("_PDT2[0-9]+.*", "_PDT2.nii.gz", ni_addEchoNum)
         print('renaming: '+k+' to '+ni_changeEnding)
         os.rename(k, ni_changeEnding)
 
@@ -43,12 +43,12 @@
         echonum = data["EchoNumber"]
 
         js_addEchoNum = re.sub("_echo_", "_echo-" + str(echonum) + "_", i)
-        js_changeEnding = re.sub("PDT2.*", "PDT2.json", js_addEchoNum)
+        js_changeEnding = re.sub("_PDT2[0-9]+.*", "_PDT2.json", js_addEchoNum)
         print('renaming: '+i+' to '+js_changeEnding)
         os.rename(i, js_changeEnding)
 
         ni_addEchoNum = re.sub("_echo_", "_echo-" + str(echonum) + "_", k)
-        ni_changeEnding = re.sub("PDT2.*", "PDT2.nii.gz", ni_addEchoNum)
+        ni_changeEnding = re.sub("_PDT2[0-9]+.*", "_PDT2.nii.gz", ni_addEchoNum)
         print('renaming: '+k+' to '+ni_changeEnding)
         os.rename(k, ni_changeEnding)
 
diff --git a/heuristics/cfmm_base.py b/heuristics/cfmm_base.py
@@ -381,7 +381,7 @@ def infotodict(seqinfo):
     #tse tra T2w
 
 
-        if ('pd_t2_tse_tra' in s.series_description): 
+        if ('pd_t2_tse_tra' in s.series_description or 'pd+t2_tse_tra' in s.series_description): 
                 if ('ND' in (s.image_type[3].strip())):
                     info[pd_t2_tse_tra].append({'item': s.series_id})
                 if ('DIS3D' in (s.image_type[3].strip())):
@@ -391,15 +391,15 @@ def infotodict(seqinfo):
 
 
                 #tse cor T2w
-        elif ('pd_t2_tse_cor' in s.series_description): 
+        elif ('pd_t2_tse_cor' in s.series_description or 'pd+t2_tse_cor' in s.series_description): 
                 if ('ND' in (s.image_type[3].strip())):
                     info[pd_t2_tse_cor].append({'item': s.series_id})
                 if ('DIS3D' in (s.image_type[3].strip())):
                     info[DIS3D_pd_t2_tse_cor].append({'item': s.series_id})
                 if ('DIS2D' in (s.image_type[3].strip())):
                     info[DIS2D_pd_t2_tse_cor].append({'item': s.series_id})
 
-        elif ('pd_t2_tse' in s.series_description): 
+        elif ('pd_t2_tse' in s.series_description or 'pd+t2_tse' in s.series_description): 
                 if ('ND' in (s.image_type[3].strip())):
                     info[pd_t2_tse].append({'item': s.series_id})
                 if ('DIS3D' in (s.image_type[3].strip())):