Hi Mathieu, look at the group analysis tutorial on our wiki. Basically, you will run mris_preproc, mri_surf2surf to smooth, then mri_glmfit to do the group analysis, then mri_glmfit-sim to do the correction for multiple comparisons. doug
On 10/21/15 10:15 AM, Mathieu Dubois wrote:
Hi,
I'm a beginner with freesurfer so I apologize if it's a trivial question.
I recently run recon-all with the -all on many subjects. As far as I can say, all the steps worked. However, the measures on the average brain (output of mris_preproc and friends) were not computed.
A colleague told me that he usually re-run recon-all with the -qcache flag to compute those. This seems to work but I don't understand if it is the recommended way to run mris_preproc and why it is not included with -all. Is it possible to get those measures in one call to recon-all?
I don't think that the issue comes from the data (e.g. that the failing of a step stops some branch of the pipeline) because it seems to run correctly with -qcache.
I haven't found any help on -qcache and the help of recon-all doesn't mention mris_preproc or mri_surf2surf.
Thanks in advance, Mathieu _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer