You'd have to issue multiple mri_surf2surf commands and then run mri_concat on all the output files to give you a stack in one file. Alternatively, you can ues mris_preproc with --targ fsaverage6

On 06/02/2016 01:20 PM, Nandita Vijayakumar wrote:

Dear FreeSurfer Experts,

I'm trying to downsample the thickness info of subjects (with longitudinal data) to the same number of vertices as fsaverage6, and would like to save this output as an mgh file for use in Matlab. I was able to downsample a single subject using the following command:

mri_surf2surf --hemi lh --srcsubject 'subjID' --srcsurfval thickness --src_type curv --trgsubject fsaverage6 --trgsurfval 'output name' --trg_type mgh

However, it won't allow me to enter multiple subject IDs into the same command. I'm wondering what's the best way to do this, with the aim of getting a single mgh file that has the thickness data for all subjects. Do I have to create a separate downsampled mgh file for each subject and then merge them?

Thanks,

Nandi

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