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 >>> _______________________________________________ >>> 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. >> > _______________________________________________ > 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
