You can, but you need to give mri_glmfit the specific label to use as a
mask (eg, --label or --mask). You can extract labels from an annot with
mri_annotation2label. Then mri_glmfit-sim will automatically restrict
the correction to that label
On 4/6/2023 10:05 AM, John Anderson wrote:
External Email - Use Caution
Dear Dr Greve,
Apologize for not providing a clear explanation earlier. The file
lh.all.suvr.sm05.proj0.5.nii.gz is the result of combining all SUVR
maps, using mri_concat, after projecting them onto the brain surface
with mri_vol2surf.
I would like to know if it is possible to use mri_glmfit-sim to
correct for specific regions of interest (such as lobes) instead of
correcting the entire brain.
I am using the following command: mri_glmfit-sim --glmdir
lh.suvr.glmdir --cache 4 pos --cwp 0.05 --2spaces
When I include the "--annot lobes" option in my command
(mri_glmfit-sim --glmdir lh.suvr.glmdir --cache 4 pos --cwp 0.05
--2spaces --annot lobes), the resulting statistical output is similar,
but the annotations are replaced with their corresponding lobes.
However, p-values are not adjusted for the number of regions of
interest specified in the "--annot" option. Thanks again
On Wed, Apr 5, 2023 at 10:46 PM Douglas N. Greve
<dgr...@mgh.harvard.edu> wrote:
What is h.all.suvr.sm05.proj0.5.nii.gz? Where did it come from?
The name looks like it might be a voxel-wise map, but you say
something about ROIs. mri_glmfit does not correct for multiple
comparisons. For ROI-based analyses, you can use bonferroni or
FDR. For maps you can use mri_glmfit-sim.
On 4/4/2023 4:53 PM, John Anderson wrote:
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Hello Freesurfer,
Currently, I am using the Petsurfer manual, which is easily
understandable and clear. Nonetheless, I have a question
regarding the "mri_glmfit" step.
As far as I know, this command is used to correct data for
multiple comparisons among all the ROIs in the aparc+aseg.mgz
file. Can you please confirm if my understanding is correct?
mri_glmfit.bin --y lh.all.suvr.sm05.proj0.5.nii.gz --fsgd
2G0C.fsgd --C patients_vs_controls.mtx --surf fsaverage lh
--cortex --glmdir lh.patinets_vs_controls
In particular, I am interested in correcting data across lobes
instead of across all ROIs. I followed the steps mentioned in the
FS forum to create lobes, and I can observe lobe annotations in
the wmparc.mgz file. I am curious to know whether using the
"--annot" flag will adjust the p-values across different lobe
ROIs instead of all ROIs in the aparc+aseg.mgz file. I have
attempted this, but it appears to only change the name of the
annotation in the final statistics file, and the p-value remains
the same. Do I need to include any additional arguments in the
command?
Thanks for your help
John
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