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> 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 > Input AD_003 AD > Input AD_005 AD > ... > Input HV_AB HV > Input HV_AE HV > > > 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> > To: 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> 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. >
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