I think that would be ok, but I would run this instead

mri_surf2surf --hemi lh --srcsubject 1001 --srcsurfval thickness --src_type curv --cortex --trgsubject fsaverage5 --trgsurfval ./mgh/1001_lh_fs5_thick.mgh --trg_type mgh –fwhm-trg 10

On 11/23/2020 4:11 PM, Daniel Leopold wrote:

External Email - Use Caution

Dear Freesurfer experts,

The mri_surf2surf example 1 specifies that lh thickness is resampled onto the 7th order icosahedron. Does it place the lh.thickness curv into freesurfer space, or is it still in the subject's native space (i.e., pre-transformation to the fsaverage template)?

I used a similar process to downsample subjects' thickness to fs5 resolution, which I then concatenated and used as input for PALM. What I'm now wondering is whether results may be due to misalignment between individual subjects because they were not transformed to the fsaverage template and space. Do the inputs below (-srcsurfval) need to be thickness.fsaverage.mgh (already mris_preproc'd in the recon-all pipeline) instead?

mri_surf2surf --hemi lh --srcsubject 1001 --srcsurfval thickness --src_type curv --cortex --trgsubject ico --trgicoorder 5 --trgsurfval ./mgh/1001_lh_fs5_thick.mgh --trg_type mgh –fwhm-trg 10

**Note: My apologies if this re-posts, but it doesn't seem like my initial submission went through**

With gratitude, Dan

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer