By default, mri_glmfit will "prune" voxels. Ie, if it finds any subject
that is zero at a given voxel, then that voxel is set to zero in the
output and in the mask. I suggest you load up your data
(lh.cbf.fsaverage.proj0.5sm00.nii.gz) as an overlay in freeview and
scroll through the subjects looking for the culprit(s).
On 9/27/2023 2:06 PM, John Anderson wrote:
External Email - Use Caution
Dear Freesurfer experts,
I am trying to run perfusion data analysis on the brain surface. I
registered images to "fsaverage" and concatenated them (following the
"petsurfer" pipeline). When I use "freeview" to visualize the
concatenated images, they appear correct.
However, when I run the "glmfit" command (as shown below), the output
appears chopped. Upon checking "mask.mgh", I believe this is the
reason the final statistical map is incorrect. I couldn't figure out
why this is happening and how to troubleshoot. I would appreciate your
guidance
mri_glmfit --y lh.cbf.fsaverage.proj0.5sm00.nii.gz --fsgd g1c0.fsgd
--C slope-.mtx --surf fsaverage lh --cortex --glmdir lh.cbf
Thanks
John
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