That looks exactly right. Are you experiencing a problem? I assume that uS1_v01_06LOC_x001.img is a mean functional image of some sort (and not a contrast image). Did you check the registration?

doug

Johannes Klackl wrote:

Dear all,

I'm currently trying to conduct a surface-based group analysis using 1st level contrast images from SPM5. I wanted to ask if somebody could tell me if what I'm doing is OK. I would relly appreciate your help!

I will now describe the procedure:

The functionals of each subject were realigned and unwarped using SPM5 preprocessing commands and then entered into an SPM 1st level designs. Additionally, of course, cortical models from all subjects were created using Freesurfer.

I used spmregister to realign the contrast images (con_0001.img) with the Freesurfer anatomicals. spmregister --s v01 --mov ../f2/auS1_v01_06LOC_x001.img --reg v01_register.dat

Then I used mri_vol2surf (with the resulting registration file from spmregister) to bring the volumetric information from the contrast images onto each subject's individual surface. mri_vol2surf --hemi lh --src con_0001.img --src_type analyze --srcreg v01_register.dat --out lh.con_0001.mgh --out_type mgh --projfrac 0.5 --noreshape

After that, I used mri_surf2surf with ico as the target to bring all the functionals from the individual subject surface onto a common surface. mri_surf2surf --hemi lh --srcsubject v01 --srcsurfval lh.con_0001.mgh --src_type mgh --trgsubject ico --trgicoorder 7 --trgsurfval lh.ico.con_0001.mgh --trg_type mgh

I was thinking about smoothing here, but I didn't do this yet.

Then, I used mri_concat to concatenate the functionals from all subjects into one file and mri_glmfit to do the statistics.

Thanks,

Johannes Klackl, University of Salzburg _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer