Merge branch 'develop'

DCAN-Labs · Jan 27, 2021 · 56f0cbb · 56f0cbb
2 parents 7c6b977 + e022a9f
commit 56f0cbb
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Showing 2 changed files with 38 additions and 6 deletions.
diff --git a/abcd2bids.py b/abcd2bids.py
@@ -69,7 +69,8 @@ def main():
     starting_timestamp = get_and_print_timestamp_when(sys.argv[0], "started")
 
     # Set cleanup function to delete all temporary files if script crashes
-    set_to_cleanup_on_crash(cli_args.temp)
+    if cli_args.remove:
+        set_to_cleanup_on_crash(cli_args.temp)
 
     # Before running any different scripts, validate user's NDA credentials and
     # use them to make NDA token
@@ -737,7 +738,7 @@ def validate_bids(cli_args):
     """
     try:
         if cli_args.sif_path:
-            subprocess.check_call(("singularity", "run", "-B", cli_args.output, 
+            subprocess.check_call(("singularity", "run", "-B", cli_args.output + ":/data", 
                                    cli_args.sif_path, "/data"))
         else:
             if cli_args.docker_cmd:

diff --git a/abcd_dcm2bids.conf b/abcd_dcm2bids.conf
@@ -64,6 +64,15 @@
                 "SeriesDescription": "ABCD-Diffusion-FM_GE_original_*"
             }
         },
+        {
+            "dataType": "fmap",
+            "modalityLabel": "epi",
+            "customLabels": "acq-dwi_dir-AP",
+            "intendedFor": 2,
+            "criteria": {
+                "SeriesDescription": "ABCD-Diffusion-FM,*"
+            }
+        },
         {
             "dataType": "fmap",
             "modalityLabel": "epi",
@@ -96,7 +105,7 @@
             "modalityLabel": "epi",
             "customLabels": "acq-func_dir-AP",
             "criteria": {
-                "SeriesDescription": "ABCD-fMRI-FM-AP*"
+                "SeriesDescription": "ABCD-fMRI-FM-AP,*"
             }
         },
         {
@@ -112,7 +121,7 @@
             "modalityLabel": "epi",
             "customLabels": "acq-func_dir-PA",
             "criteria": {
-                "SeriesDescription": "ABCD-fMRI-FM-PA*"
+                "SeriesDescription": "ABCD-fMRI-FM-PA,*"
             }
         },
         {
@@ -136,7 +145,14 @@
             "modalityLabel": "T1w",
             "customLabels": "rec-normalized",
             "criteria": {
-                "SeriesDescription": "ABCD-T1-NORM*"
+                "SeriesDescription": "ABCD-T1-NORM,*"
+            }
+        },
+        {
+            "dataType": "anat",
+            "modalityLabel": "T1w",
+            "criteria": {
+                "SeriesDescription": "ABCD-T1,*"
             }
         },
         {
@@ -166,7 +182,14 @@
             "modalityLabel": "T2w",
             "customLabels": "rec-normalized",
             "criteria": {
-                "SeriesDescription": "ABCD-T2-NORM*"
+                "SeriesDescription": "ABCD-T2-NORM,*"
+            }
+        },
+        {
+            "dataType": "anat",
+            "modalityLabel": "T2w",
+            "criteria": {
+                "SeriesDescription": "ABCD-T2,*"
             }
         },
         {
@@ -303,6 +326,14 @@
                 "SeriesDescription": "ABCD-fMRI-FM_GE_original_*"
             }
         },
+        {
+            "dataType": "fmap",
+            "modalityLabel": "epi",
+            "customLabels": "acq-func_dir-both",
+            "criteria": {
+                "SeriesDescription": "ABCD-fMRI-FM,*"
+            }
+        },
         {
             "dataType": "anat",
             "modalityLabel": "T1w",