I think palm itself requires mgh or mgz files. I can't remember why we don't convert it. You can run mri_glmfit with --mgz or --mgh (or just without --nii.gz) and it should work.

On 9/9/2019 9:24 AM, Barbour, Tracy,M.D. wrote:

Hello Freesurfer community!

I am trying to run fspalm on surface based data. I have installed PALM, fspalm, mri_surfcluster, and mri_volcluster.

This is my fspalm command:

fspalm --glmdir TEPSC.glmdir --cft 1.3 --twotail --name palm-twotail-1.3 --iters 1000 --2spaces --cwp .05

When I run the fspalm command I get the error: "for surface based analysis, input cannot be nii or nii.gz"

I thought that fspalm was supposed to convert ces.nii.gz files into something that PALM could use.

Please let me know if there is another step I need to run or if I need to change the script.

Best,

Tracy
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