Rui Sun

Rui Sun

Ph.D. student
Biomedical Engineering
Carnegie Mellon University

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title: ‘Downsample pial surfaces in Freesurfer’ date: 2020-10-12 permalink: /posts/2020/10/fs_ds/ categories:

  • Tools

Downsample a pial surface

To downsample a pial surface that was mapped to the original MRI space (rawavg.mgz), use

mri_surf2surf --srcsubject <xxx> --trgsubject ico --trgicoorder 5 --hemi lh --sval-xyz native.pial --tval lh.ds.native.pial --tval-xyz mri/rawavg.mgz

in the $SUBJECTS_DIR/<xxx> folder. The high resolution pial cortex *h.native.pial is saved in surf/ folder. The generated surface will be saved in the subject folder. Similarly, for the original pial surface

mri_surf2surf --srcsubject <xxx> --trgsubject ico --trgicoorder 5 --hemi lh --sval-xyz pial --tval lh.ds.pial --tval-xyz mri/T1.mgz

Downsample a annot file

mri_surf2surf --srcsubject <xxx> --trgsubject ico --trgicoorder 5 --hemi rh --sval-annot xxx.annot --tval $SUBJECTS_DIR/EP1095_Pre_fs/label/rh.xxx.annot

Updated: