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 On Sat, Mar 5, 2016 at 2:01 AM, 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 >
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