No, we will continue to support it On 10/21/2015 11:13 PM, 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 >>>> _______________________________________________ >>>> 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 > >
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
