Dear Douglas, 1) Does this beta version of FS 6 (freesurfer-Linux-centos6_x86_64-stable-v6-beta-20151015.tar.gz) also have problems with the individual data analysis or the volumetric group analysis, e.g. the files in the stats/ folder for each subject?
2) So could I use the results of these surface-based group analyses after running the "-qcache" on the latest "-dev" version (freesurfer-Linux-centos6_x86_64-dev-20160315) available today on the website then? I tried one data for "-qcache" with this latest -dev version, and see the files of ?h.area.fwhm10... and ?h.thickness.fwhm10... are different now (mri_diff), but still the same between ?h.area.fwhm10... and ?h.area.pial.fwhm10... . Is it right? 3) How about the hippocampus and brainstem sub-structure analyses, are there changes on these features within different beta versions too? Thanks, Kaiming On 15 March 2016 at 18:00, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > this only has to do with the qcache part of recon-all, so you could use > version 5.3 recon-all -qcache and it should be fine. However, it is not a > good idea to try to publish using the analysis from the version of FS that > you used. That was a beta version of version 6 and things will change. > > > On 03/15/2016 01:56 PM, Kaiming Yin wrote: > >> Dear Douglas, >> >> Is there anything I can do now to fix this now? I don't want to re-run >> all the data again. >> >> Thanks, >> Kaiming >> >> >> On 15 March 2016 at 16:53, Douglas N Greve <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> >> OK, this is a bug that I found and fixed in early Nov. Sorry, >> that's part of the danger of using a beta version. >> >> On 03/14/2016 12:22 PM, Kaiming Yin wrote: >> >> Dear Douglas, >> >> I re-run the "-qcache" on one data and it took 8 mins to >> finish. Still the files are the same, all in 668.6kB size. >> >> >> Kaiming >> >> On 14 March 2016 at 15:56, Douglas Greve >> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: >> >> I don't know what happened. I cannot replicate it here. >> Can you >> re-run the recon-all -s -qcache command and verify that >> the files >> are still the same? >> >> >> On 3/14/16 11:11 AM, Kaiming Yin wrote: >> >> Dear Douglas, >> >> Yes, both of the two pairs of files are the same. i.e. >> >> mri_diff rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh >> >> diffcount 0 >> >> >> mri_diff rh.thickness.fwhm10.fsaverage.mgh >> rh.area.fwhm10.fsaverage.mgh >> >> diffcount 0 >> >> >> Does this mean I run the "-qcache" wrongly? I just run >> "recon-all >> -s XX -qcache" on each subject. >> >> Thanks, >> Kaiming >> >> >> On 14 March 2016 at 14:58, Douglas Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: >> >> Check whether rh.ad_hv.thick.10.mgh and >> rh.ad_hv.area.10.mgh >> are the same, ie, >> mri_diff rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh >> >> If those are the same, then check whether >> thickness.fwhm10.fsaverage and >> area.fwhm10.fsaverage are the >> same in each subject >> >> >> On 3/14/16 10:53 AM, Kaiming Yin wrote: >> >> Dear Douglas, >> >> My command lines were, e.g. right thickness >> and right white >> surface (using the same ad_hv.fsgd and >> group_diff.mtx files >> in the command lines): >> >> >> ad_hv.fsgd >> >> GroupDescriptorFile 1 >> Title AD_HV_GroupAnalysis >> Class AD >> Class HV >> InputAD_003AD >> InputAD_005AD >> ... >> InputHV_ABHV >> InputHV_AEHV >> >> >> group_diff.mtx >> >> 1 -1 >> >> >> right thickness >> >> mris_preproc --fsgd ad_hv.fsgd --cache-in >> thickness.fwhm10.fsaverage --target fsaverage >> --hemi rh >> --out rh.ad_hv.thick.10.mgh >> >> mri_glmfit --y rh.ad_hv.thick.10.mgh --fsgd >> ad_hv.fsgd dods >> --C group_diff.mtx --surf fsaverage rh >> --cortex --glmdir >> rh.ad_hv.thick.glmdir >> >> mri_glmfit-sim --glmdir rh.ad_hv.thick.glmdir >> --cache 4 neg >> --cwp 0.05 --2spaces >> >> >> right white surface >> >> mris_preproc --fsgd ad_hv.fsgd --cache-in >> area.fwhm10.fsaverage --target fsaverage >> --hemi rh --out >> rh.ad_hv.area.10.mgh >> >> mri_glmfit --y rh.ad_hv.area.10.mgh --fsgd >> ad_hv.fsgd dods >> --C group_diff.mtx --surf fsaverage rh >> --cortex --glmdir >> rh.ad_hv.area.glmdir >> >> mri_glmfit-sim --glmdir rh.ad_hv.area.glmdir >> --cache 4 neg >> --cwp 0.05 --2spaces >> >> >> Their results were all the same. >> >> Thanks, >> Kaiming >> >> >> ---------- Forwarded message ---------- >> From: Douglas N Greve >> <gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>> >> To: freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu> >> <mailto:freesurfer@nmr.mgh.harvard.edu >> <mailto:freesurfer@nmr.mgh.harvard.edu>> >> Cc: >> Date: Mon, 7 Mar 2016 18:47:11 -0500 >> Subject: Re: [Freesurfer] group analysis all >> measures same >> results >> what are your command lines? >> >> >> On 5 March 2016 at 02:01, Kaiming Yin >> <yinkaiming6...@gmail.com >> <mailto:yinkaiming6...@gmail.com> >> <mailto:yinkaiming6...@gmail.com >> >> <mailto:yinkaiming6...@gmail.com>>> >> >> wrote: >> >> Dear guys, >> >> I was doing group analysis (command-line) >> on two groups >> (patients and control, no age or other >> information). The >> data has been "qcached", and after >> following the three >> steps as "mris_preproc, mri_glmfit and >> mri_glmfit-sim" >> shown in the tutorial on the Freesurfer >> website, I >> obtained the difference on thickness in >> both left and >> right hemispheres, which seems great. >> However, when I >> repeated the above steps on other >> measures, e.g. area, >> area.pial, volume (also replaced the parts of >> "thickness" in the command lines), the >> results seemed to >> be exactly the same again as those in the >> thickness >> comparison, even the p-value numbers in >> the file >> "cache.th40.neg.sig.cluster.summary" were >> the same. I >> was using Freesurfer v6.0-beta, and I >> performed the >> individual data analysis on a linux >> cluster and I >> copied/downloaded the whole "qcached" >> subject directory >> to my linux laptop to perform the group >> comparison, both >> using the same version of Freesurfer, does >> it matter? Or >> do you know why it happened like this? >> >> Thanks, >> Kaiming >> >> >> >> 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. >> >> >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> Fax: 617-726-7422 <tel:617-726-7422> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> > -- > 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 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.
