On 10/8/17 10:06 AM, Jonathan Bain wrote:
Dear FreeSurfer community,
For a template subject (Colin27), I have a volumetric atlas (nifti file, where each brain region is numbered 1, 2, 3...). I am trying to use FreeSurfer to get the volumetric atlas into volumetric subject space (moving through surface-based registration).
I have tried two approaches, but neither has worked satisfactorily.
First, I used mri_vol2surf to move from the Colin27 volume to the subject surface. This was problematic because the output contained fractional labels (e.g. 2.33), and the labeled regions also had holes in them.
Use --interp nearest (or don't use --interp trilin)
Second, I used mris_sample_parc to move from the Colin27 volume to annotation files. When overlaid atop the FreeSurfer inflated surface, the output regions were not at all where they were supposed to be. I checked the sform of the original nifti and noticed that the first row was negative (flip in the x-direction), but the error persisted when I flipped the data and changed the sform first row to positive.
I already have run recon-all for Colin27 and for my subjects. I am using freesurfer-Linux-centos6_x86_64-dev-20160903-5b25567.
I have looked through the archive but have not found this question addressed. If you have any suggestions for how to do this, I would greatly appreciate it!
Thank you,
Jonathan
The commands I am using:
- First: mri_vol2surf --mov /path/to/Juelich-maxprob-thr0-1mm.nii.gz --trgsubject 002_KM --o /path/to/002_KM/mri/lh.julich_label.mgz --hemi lh --mni152reg --interp nearest
- Second: mris_sample_parc -ct /path/to/freesurfer/FreeSurferColorLUT.txt colin27 lh /path/to/Juelich-maxprob-thr0-1mm.nii.gz colinJUE_lh.annot
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