[Freesurfer] surface based analysis and mask.mgh

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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