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 <gr...@nmr.mgh.harvard.edu
<mailto:gr...@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 <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
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