Re: [Freesurfer] group analysis all measures same results

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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> To: 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 <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