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
