Hi Mathieu

I don't see any reason we wouldn't continue to support it
Bruce
On Thu, 22 Oct 2015, Mathieu Dubois wrote:

Hi again,

Another advantage of using qcache in my case is that the file names are
automatically generated and therefore standard.

Is there any risk (particularly for future compatibility) in using
qcache? Did anyone had some problem with it?

Thanks in advance,
Mathieu

Le 21/10/2015 18:07, Mathieu Dubois a écrit :

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
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