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 > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
