Hello all,

I want to run a Monte Carlo simulation within a volume ROI and I am running into a problem when I use the --mask flag while running glmfit. My question is very similar to the question asked in "[Freesurfer] Volume-based Monte Carlo Restricted to a within mask area" but I could not find the response to this question.

Here is my code.

First, I created a volume mask with mri_binarize:

mri_binarize --match 18 --i home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/fsaverage/mri/aseg.mgz --o /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz

I checked the mask and it looked good. Then I use the mask in glmfit.

mri_glmfit --y ces.nii.gz --osgm --glmdir glm.amygdala_lh --mask /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz

When I do this, I get the following error:

ERROR: dimension mismatch 1 between y and mask

I guess this means that the ces.nii.gz file and mask file don't match, but I have no idea how to solve this. Any thoughts?

Thanks!

Suzanne

Suzanne Oosterwijk, Ph.D.

Postdoctoral Researcher

Department of Social Psychology

University of Amsterdam

s.oosterwijk@u va.nl

https://sites.google.com/site/suzanneoosterwijk/