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FIX: Avoid diverting CIFTI dtype from original BOLD #532

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Merged
merged 2 commits into from
Jun 9, 2020
Merged

FIX: Avoid diverting CIFTI dtype from original BOLD #532

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c5a257f
FIX: Avoid diverting dtype from original
mgxd Jun 2, 2020
915cb01
ENH: apply changes from @effigies review
mgxd Jun 2, 2020
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11 changes: 6 additions & 5 deletions niworkflows/interfaces/cifti.py
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Original file line number Diff line number Diff line change
Expand Up @@ -330,6 +330,7 @@ def _create_cifti_image(
BOLD data saved as CIFTI dtseries
"""
bold_img = nb.load(bold_file)
bold_dtype = bold_img.get_data_dtype()
label_img = nb.load(label_file)
if label_img.shape != bold_img.shape[:3]:
warnings.warn("Resampling bold volume to match label dimensions")
Expand All @@ -339,7 +340,7 @@ def _create_cifti_image(
bold_img = _reorient_image(bold_img, orientation="LAS")
label_img = _reorient_image(label_img, orientation="LAS")

bold_data = bold_img.get_fdata(dtype="float32")
bold_data = bold_img.get_fdata()
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@effigies effigies Jun 2, 2020

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Is there a good reason to upcast to float64?

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@mgxd mgxd Jun 2, 2020

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nope, can revert that

timepoints = bold_img.shape[3]
label_data = np.asanyarray(label_img.dataobj).astype("int16")

Expand All @@ -355,7 +356,7 @@ def _create_cifti_image(
hemi = structure.split("_")[-1]
# currently only supports L/R cortex
surf = nb.load(bold_surfs[hemi == "RIGHT"])
surf_verts = len(surf.darrays[0].data)
surf_verts = len(surf.agg_data()[0])
if annotation_files[0].endswith(".annot"):
annot = nb.freesurfer.read_annot(annotation_files[hemi == "RIGHT"])
# remove medial wall
Expand Down Expand Up @@ -391,7 +392,7 @@ def _create_cifti_image(
else np.concatenate((ts, bold_data[ijk]))
)
vox += [
[ijk[0][ix], ijk[1][ix], ijk[2][ix]] for ix, row in enumerate(ts)
[ijk[0][idx], ijk[1][idx], ijk[2][idx]] for idx in range(len(ts))
]

vox = ci.Cifti2VoxelIndicesIJK(vox)
Expand All @@ -403,7 +404,7 @@ def _create_cifti_image(
voxel_indices_ijk=vox,
)
idx_offset += len(vox)
bm_ts = np.column_stack((bm_ts, ts.T))
bm_ts = np.column_stack((bm_ts, ts.T)).astype(bold_dtype)
# add each brain structure to list
brainmodels.append(bm)

Expand Down Expand Up @@ -439,7 +440,7 @@ def _create_cifti_image(
matrix.append(geometry_map)
matrix.metadata = ci.Cifti2MetaData(meta)
hdr = ci.Cifti2Header(matrix)
img = ci.Cifti2Image(bm_ts, hdr)
img = ci.Cifti2Image(dataobj=bm_ts, header=hdr, nifti_header=bold_img.header)
img.nifti_header.set_intent("NIFTI_INTENT_CONNECTIVITY_DENSE_SERIES")

out_file = "{}.dtseries.nii".format(split_filename(bold_file)[1])
Expand Down