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:

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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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