Using segmentation files in place of T1w


I was wondering if segmentation files (in vtk or NIFTI format) can be added into the processing pipeline in place of using the T1 NIFTI files?

Any suggestions you have is greatly appreciated.

Thank you!

Hi @rhi,

Thanks for reaching out. This is actually possible you can take a look at the example jobfile (osprey/exampledata/sdat/UnEdited/jobSDAT.m) to see how to do this. See also both screenshots below.

You have to add the gray matter, white matter, and CSF binary masks as separate .nii or .nii.gz files in the specified order or as a single 4D NIfTI in the same order. This is done by adding a files_sep cell array in the jobfile.

In the automatic loop for BIDS formatted data:

Or by directly defining the path to the files:

Afterward, Osprey should take care of the rest. For the T1 NIfTI files, you have to add the NII image that the masks were derived from or at least an NII image with the same resolution and orientation because Osprey uses this to perform the co-registration of the MRS voxel.

Let me know how this works out.