Wednesday, October 19, 2016

note on the subcortical part of CIFTIs

As people working with HCP CIFTI images know, the cortex is represented by (surface) vertices, but subcortical structures as voxels. As I explained before, you can use the wb_command -cifti-separate to make a volumetric NIfTI of a subcortical structure (say AMYGDALA_LEFT). The HCP minimally preprocessing pipelines create the CIFTI versions of each (task, in my case) run and also volumetric NIfTI versions. So my question: is timecourse of a voxel in a subcortical structure the same when taken out of an unpacked CIFTI and a NIfTI? Answer: no.

This screenshot shows the volumetric NIfTI (red stripe),
 AMYGDALA_LEFT via wb_command -cifti-separate (green stripe), and the _AtlasSubcortical_s2.nii.gz image (yellow stripe) for one of our HCP pipeline minimally-processed task fMRI runs.

The _AtlasSubcortical_s2.nii.gz image was created by the pipeline, and looks to be the subcortical (volumetric) part of the CIFTI: the value at this voxel is identical (green and yellow). The value for the voxel in the volumetric NIfTI (red) is a bit different, however.

Note that I don't think this mismatch is an error: parcel-constrained smoothing is done during the HCP pipelines that make the CIFTIs (e.g., Glasser et al. 2013), and I suspect that this smoothing accounts for the different voxel values. However, it's good to be aware of the additional processing: if you're doing a volumetric analysis with HCP-type preprocessing, it matters whether you take the subcortical structures out of the CIFTI or the NIfTI.

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