Hi Asim, I ran into some issues on my test. I think the software is
doing what it is supposed to do, but I think there is something wrong
with the underlying permutation method when using PVRs. This will take a
while for me to figure out. In the meantime, you can try using the more
conventional mcz correction. If the cluster p-value is very strong, then
the liberalness of the method might not matter.
On 2/22/2022 5:32 PM, Dhungana, Asim wrote:
Thank you! I ran the development version of the mri_glmfit-sim command
on my data, and it did not crash and seems to give reasonable outputs
(smaller clusters disappear after correction). Whenever your tests are
done, it will be good to know if they confirm that everything is working.
Best,
Asim
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Monday, February 21, 2022 6:29 PM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] mri_glmfit of surface CBF maps while
regressing out cortical thickness
I just updated the code to accept PVRs. I'm not sure what I have to do
to test it; I guess I need to run the null test like I did for the
non-PVR version. This will take a while. In the mean time, can you
download the development version and just try it on your data to see
if it crashes or gives results that don't seem to make sense? You'll
have to wait until the development version is updated (probably tomorrow).
On 2/17/2022 5:22 PM, Dhungana, Asim wrote:
Hello Doug, just following up on my questions below on how/if I can
correct for multiple comparisons with PVR. Thanks again.
Best,
Asim
------------------------------------------------------------------------
*From:* Dhungana, Asim <adhung...@mgh.harvard.edu>
<mailto:adhung...@mgh.harvard.edu>
*Sent:* Monday, February 14, 2022 11:45 AM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] mri_glmfit of surface CBF maps while
regressing out cortical thickness
OK, I see. How would you recommend correcting for multiple
comparisons if the perm option does not work with PVR?
Also, are you saying that I should only use the glm.osgm.lh/eres.mgh
file as a pvr argument? Does this look correct:
mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr glm.osgm.lh/eres.mgh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save
Best,
Asim
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas
N. Greve <dgr...@mgh.harvard.edu> <mailto:dgr...@mgh.harvard.edu>
*Sent:* Sunday, February 13, 2022 5:29 PM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* Re: [Freesurfer] mri_glmfit of surface CBF maps while
regressing out cortical thickness
Re: long run time. Sorry, permutation will not work with PVR.
Re: mean thickness. Use the eres.mgh from you osgm analysis instead
of the raw thickness map (lh.thickness.fwhm10.mgh)
On 2/8/2022 4:12 PM, Dhungana, Asim wrote:
Dear Freesurfer experts,
I am trying to run a GLM analysis comparing the difference in the
cortical CBF maps between two groups, but I would like to regress
out cortical thickness. I read through a post with a similar
question
(https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65059.html
<https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg65059.html>),
but I am still a little confused and want to confirm the steps of my
analysis below:
---
1. Compile/smooth CBF data on surface for all subjects.
mris_preproc
--hemi lh \
--projfrac 0.5 \
--target fsaverage \
--o lh.cbf.00.mgh \
--iv subj1/cbf.mgz subj1/register_pasl.dat \
--iv subj2/cbf.mgz subj2/register_pasl.dat \
... until subjN
mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.cbf.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.cbf.fwhm10.mgh
2. Compile/smooth thickness data on surface for all subjects.
mris_preproc \
--fsgd cbf.fsgd \
--target fsaverage \
--hemi lh \
--meas thickness \
--out lh.thickness.00.mgh
mri_surf2surf \
--hemi lh \
--s fsaverage \
--sval lh.thickness.00.mgh \
--fwhm 10 \
--cortex \
--tval lh.thickness.fwhm10.mgh
3. GLM fit of CBF maps, including thickness as a regressor.
mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr lh.thickness.fwhm10.mgh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save
4. Multiple comparisons correction
mri_glmfit-sim \
--glmdir lh.cbf.fwhm10.glmdir \
--perm 1000 1.3 abs \
--cwp 0.05 \
--2spaces \
--bg 35
---
I am currently having issues with Step 4; it has been over an hour,
and it seems that the command will not finish executing. It is also
not outputting any error messages. Whenever I run this analysis
using the same parameters but without regressing out thickness, this
step takes under five minutes on my machine and returns appropriate
results. It seems like I must be doing something wrong, but I'm not
sure. Please let me know if there is anything that you would
change/add above.
Also, I noticed that you recommended regressing out the overall mean
thickness (which you can obtain through mri_glmfit --surf fsaverage
lh --osgm --y lh.thickness.fwhm10.mgh --o glm.osgm.lh --eres-save).
Is glm.osgm.lh the mean stratified by class or the overall mean? If
I were to include this in my GLM fit, would this be the correct command:
mri_glmfit \
--y lh.cbf.fwhm10.mgh \
--fsgd cbf.fsgd \
--pvr lh.thickness.fwhm10.mgh glm.osgm.lh \
--C contrast.ctx \ # where contrast.ctx = "1 -1 0 0"
--surf fsaverage lh \
--cortex \
--glmdir lh.cbf.fwhm10.glmdir \
--eres-save
Thank you for taking a look at this, let me know if you need any
other information.
Best,
Asim Dhungana
Freesurfer version:
freesurfer-linux-centos7_x86_64-7.1.0-20200511-813297b
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