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ENH: Ensure subcortical CIFTI is in LAS orientation #484

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Mar 20, 2020
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ENH: Ensure subcortical CIFTI is in LAS orientation #484

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4 changes: 3 additions & 1 deletion niworkflows/interfaces/cifti.py
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Expand Up @@ -318,7 +318,9 @@ def _create_cifti_image(bold_file, label_file, bold_surfs, annotation_files, tr,
warnings.warn("Resampling bold volume to match label dimensions")
bold_img = resample_to_img(bold_img, label_img)

bold_img = _reorient_image(bold_img, target_img=label_img)
# ensure images match HCP orientation (LAS)
bold_img = _reorient_image(bold_img, orientation='LAS')
label_img = _reorient_image(label_img, orientation='LAS')
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Is this going to be the case for all label files? Should we have a table mapping space to orientation?

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yes, since the final output should always be in LAS we want to ensure both BOLD / labels are as well prior to setting the IJK voxels

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I guess my reading of Tim's response was that LAS was an accident of the orientation of a specific template. Are we guaranteed that all templates HCP ever uses will be in LAS?

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no, we aren't - but that seems excessive for us to worry about. I'd rather mirror the outputs generated from HCP Pipelines, which happen to include the volume in LAS orientation


bold_data = bold_img.get_fdata(dtype='float32')
timepoints = bold_img.shape[3]
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