Hi Doug,
Thanks for your answer.
If I understand correctly, the tutorial describes the use of mris_preproc with a group description file. If the data has not been cached, it will compute them and stack all the results in a big file (will it write individual files?) . Of course if the data has been cached, it will only stack them (this probably result in more disk usage but that's OK).
I don't plan to use FreeSurfer's linear model for group analysis (my goal is to use those data in machine learning algorithms) but other people at the institute I work for may be interested in that. I think it's more convenient to have one file per subject (so I can group them in a more flexible way).
So I guess I can always run recon-all for each subject with -qcache (I have read that is safe to do so) in order to generate the data for each subject (this can easily be distributed across a cluster and compute several measures). I can then load the data for each subject and people interested into running FreeSurfer group analysis can also use them. Is it correct?
My only concern is: will -qcache be supported in future versions of FreeSurfer? Couldn't some part of it (like the resampling on the average subject but no the smoothing) be integrated into -all?
Mathieu
Le 21/10/2015 16:37, Douglas Greve a écrit :
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
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