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), 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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