Dear Douglas, Sorry for this, but could I ask how to include the previous correspondence? I just saw your responses from Freesurfer Digest, Vol 145, Issue 19, and I don't know how to do that. I use gmail.
Best, Kaiming On Tue, Mar 8, 2016 at 10:50 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > Kaiming, can you include my previous correspondence with your email? > > > On 03/08/2016 05:48 PM, 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 >> >> >> On Sat, Mar 5, 2016 at 2:01 AM, Kaiming Yin <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 >> >> >> > -- > 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/ > > > > 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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