mri_surf2surf maps to fsaverage by finding the vertex in the subject's sphere.reg that is closest to a vertex in fsaverage's sphere.reg. The only way to do this on a vertex by vertex basis is to create a "label" file with your vertices of interest, then use mri_label2label with the "--norevmap" option and "--regmethod surface".

To create an asc file to find out which vertex maps to which annotation, you can run the following routines: 1. First convert the annotation to a segmentation: mri_annotation2label --s subject --hemi lh --annotation aparc --seg lh.aparc.mgh 2. Convert the segmentation into an ascii file: mris_convert -c ./lh.aparc.mgh ../surf/lh.white lh.aparc.asc

The first col of this file will have the vertex number, the last column will have an index:

008 -11.38107 -83.52708 4.57252 1011.00000

In this case, index 1011 indicates ctx-lh-lateraloccipital, as found in $FREESURFER_HOME/FreeSurferColorLUT.txt

doug

orangekic wrote:

Hi,

Could someone tell me the way how 'mri_surf2surf' resample one subject onto fsaverage? How can I know the specific point comes from in the native space?

for example: [subject A] vertex index 1, (x, y, z) ---------<mri_surf2surf>--------> [subject A in subject B coordinate] vertex index ??, (x', y', z')

I'm using 'mris_convert' to convert the thickness file to ascii format, include vertex index, (x, y, z), and thickness information. I'm wondering that what's the rule to sort the vertex index?

And, how can I know the relationship between vertex index and the label other than in tksurfer or tkmedit?

Best

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