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Previous neurostars and NiiVue issues noted that FreeSurfer uses proprietary transforms for the open GIfTI format. It turns out that the internal proprietary FreeSurfer mesh format also stores transforms in a footer. While it is understandable that proprietary formats may include private featues, this footer is ignored by popular tools like bioelectromagnetism and spm.
import nibabel as nb
fsh = nb.freesurfer.io.read_geometry('lh.pial',True)
fsh[2]['cras']
If one loads a FreeSurfer mesh onto a FreeSurfer voxel based image, one must apply the same transform to both. Since NiiVue applies this tranform to voxels, it must also read the undocumented footer.
The text was updated successfully, but these errors were encountered:
Previous neurostars and NiiVue issues noted that FreeSurfer uses proprietary transforms for the open GIfTI format. It turns out that the internal proprietary FreeSurfer mesh format also stores transforms in a footer. While it is understandable that proprietary formats may include private featues, this footer is ignored by popular tools like bioelectromagnetism and spm.
nibabel can read these footers. For example, to read the RAS translation from the central voxel to the RAS center of the image (aka Pxyz_c) with Python:
If one loads a FreeSurfer mesh onto a FreeSurfer voxel based image, one must apply the same transform to both. Since NiiVue applies this tranform to voxels, it must also read the undocumented footer.
The text was updated successfully, but these errors were encountered: