Hi Subha, there are tools to do this in FS. You can use mri_vol2surf to map your time courses to the surface and save the output as a gifti (eg, mri_vol2surf --mov f.nii.gz --reg register.dof6.dat --hemi lh --o junk.gii --projfrac 0.5)

Or you can use the FS functional analysis stream (FSFAST). Tutorial is here:

http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1

doug

On 06/04/2013 07:07 AM, Subhabrata Chaudhury wrote:

Hello All, I have run recon-all on some subjects. I have functional BOLD data on these subjects too. I am doing fmri preprocessing in spm. I have created register.dat by registering the meanBOLD image to the freesurfer reconstructed data. I am intending to do the following - I want to take each functional volume corresponding to each TR and move each volume to freesurfer and make a BOLD surface file in freesurfer (.mgh file). Then I want to run first level glm on the data like its done for volume data in spm, fsl, afni etc. My question is are there tools in freesurfer to do this on surfaces ? If not, can the mgh file be converted to a gifti file and maybe it can be used to make first level glms in afni, spm or fsl ? I will really appreciate your opinion about this. Thank you very much, Subha

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