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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

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

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 mailto: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
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

The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.