Merge pull request #728 from UNFmontreal/fix/ge_multiecho_bvals

properly remove GE multiecho bvals/bvecs

heudiconv/convert.py

@@ -15,6 +15,7 @@
 
 import filelock
 from nipype import Node
+from nipype.interfaces.base import TraitListObject
 
 from .bids import (
     BIDS_VERSION,
@@ -880,19 +881,19 @@ def save_converted_files(
         return []
 
     if isdefined(res.outputs.bvecs) and isdefined(res.outputs.bvals):
+        bvals, bvecs = res.outputs.bvals, res.outputs.bvecs
+        bvals = list(bvals) if isinstance(bvals, TraitListObject) else bvals
+        bvecs = list(bvecs) if isinstance(bvecs, TraitListObject) else bvecs
         if prefix_dirname.endswith("dwi"):
             outname_bvecs, outname_bvals = prefix + ".bvec", prefix + ".bval"
-            safe_movefile(res.outputs.bvecs, outname_bvecs, overwrite)
-            safe_movefile(res.outputs.bvals, outname_bvals, overwrite)
+            safe_movefile(bvecs, outname_bvecs, overwrite)
+            safe_movefile(bvals, outname_bvals, overwrite)
         else:
-            if bvals_are_zero(res.outputs.bvals):
-                os.remove(res.outputs.bvecs)
-                os.remove(res.outputs.bvals)
-                lgr.debug(
-                    "%s and %s were removed since not dwi",
-                    res.outputs.bvecs,
-                    res.outputs.bvals,
-                )
+            if bvals_are_zero(bvals):
+                to_remove = bvals + bvecs if isinstance(bvals, list) else [bvals, bvecs]
+                for ftr in to_remove:
+                    os.remove(ftr)
+                lgr.debug("%s and %s were removed since not dwi", bvecs, bvals)
             else:
                 lgr.warning(
                     DW_IMAGE_IN_FMAP_FOLDER_WARNING.format(folder=prefix_dirname)
@@ -901,8 +902,8 @@ def save_converted_files(
                     ".bvec and .bval files will be generated. This is NOT BIDS compliant"
                 )
                 outname_bvecs, outname_bvals = prefix + ".bvec", prefix + ".bval"
-                safe_movefile(res.outputs.bvecs, outname_bvecs, overwrite)
-                safe_movefile(res.outputs.bvals, outname_bvals, overwrite)
+                safe_movefile(bvecs, outname_bvecs, overwrite)
+                safe_movefile(bvals, outname_bvals, overwrite)
 
     if isinstance(res_files, list):
         res_files = sorted(res_files)
@@ -1064,7 +1065,7 @@ def add_taskname_to_infofile(infofiles: str | list[str]) -> None:
         save_json(infofile, meta_info)
 
 
-def bvals_are_zero(bval_file: str) -> bool:
+def bvals_are_zero(bval_file: str | list) -> bool:
     """Checks if all entries in a bvals file are zero (or 5, for Siemens files).
 
     Parameters
@@ -1077,6 +1078,10 @@ def bvals_are_zero(bval_file: str) -> bool:
     True if all are all 0 or 5; False otherwise.
     """
 
+    # GE hyperband multi-echo containing diffusion info
+    if isinstance(bval_file, list):
+        return all(map(bvals_are_zero, bval_file))
+
     with open(bval_file) as f:
         bvals = f.read().split()
 

heudiconv/tests/data/non_zeros.bval

@@ -0,0 +1 @@
+1000 0  1000 2000

heudiconv/tests/data/zeros.bval

@@ -0,0 +1 @@
+ 0 0 0 0

heudiconv/tests/test_convert.py

@@ -14,6 +14,7 @@
 import heudiconv.convert
 from heudiconv.convert import (
     DW_IMAGE_IN_FMAP_FOLDER_WARNING,
+    bvals_are_zero,
     update_complex_name,
     update_multiecho_name,
     update_uncombined_name,
@@ -287,3 +288,16 @@ def mock_populate_intended_for(
     else:
         # If there was no heuristic, make sure populate_intended_for was not called
         assert not output.out
+
+
+def test_bvals_are_zero() -> None:
+    """Unit testing for heudiconv.convert.bvals_are_zero(),
+    which checks if non-dwi bvals are all zeros and can be removed
+    """
+    zero_bvals = op.join(TESTS_DATA_PATH, "zeros.bval")
+    non_zero_bvals = op.join(TESTS_DATA_PATH, "non_zeros.bval")
+
+    assert bvals_are_zero(zero_bvals)
+    assert not bvals_are_zero(non_zero_bvals)
+    assert bvals_are_zero([zero_bvals, zero_bvals])
+    assert not bvals_are_zero([non_zero_bvals, zero_bvals])