That should have worked, but I would use the method on this page https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 6/6/2024 4:07 PM, Nina Rouhani wrote:
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hello!
after freesurfer segmentation (through fmriprep v23), i converted the aparc+aseg.mgz file into a nifty file using the below code (freesurfer v7.4.1): -rl $fs_dir/mri/rawavg.mgz -rt nearest $fs_dir/mri/aparc+aseg.mgz $sub_dir/rois/anatomical/aparc_aseg2mprage.nii.gz
however, the voxel values of the aparc_aseg2mprage.nii.gz range between 31000-32000 and -31000- -32000. consequently, the label values for particular regions no longer correspond to what’s in the freesurfer manuals (like those listed here: FsTutorial/AnatomicalROI/FreeSurferColorLUT - Free Surfer Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT).
would be incredibly grateful if i could be pointed to what i’m missing or what could be going wrong! thank you!
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