Dear Douglas,
I will run on one data again for the "qcache". Also attached the recon-all.log script, in the end of the file lists the qcache steps.
Will let you know once this is finished.
Thanks, Kaiming
On 14 March 2016 at 15:56, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
I don't know what happened. I cannot replicate it here. Can you re-run the recon-all -s -qcache command and verify that the files are still the same?
On 3/14/16 11:11 AM, Kaiming Yin wrote:
Dear Douglas,
Yes, both of the two pairs of files are the same. i.e.
mri_diff rh.ad_hv.thick.10.mgh rh.ad_hv.area.10.mgh
diffcount 0
mri_diff rh.thickness.fwhm10.fsaverage.mgh rh.area.fwhm10.fsaverage.mgh
diffcount 0
Does this mean I run the "-qcache" wrongly? I just run "recon-all -s XX -qcache" on each subject.
Thanks, Kaiming
On 14 March 2016 at 14:58, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
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 Input AD_003 AD Input AD_005 AD ... Input HV_AB HV Input HV_AE HV
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 greve@nmr.mgh.harvard.edu> To: 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 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
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