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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