Great, thanks for your answer. Le 22/10/2015 17:42, Douglas N Greve a écrit : > 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 >> >>
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