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 greve@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 <yinkaiming6987@gmail.com mailto:yinkaiming6987@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 greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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