Hi suzanne, you'll need to use the 2mm version fsaverage/mri.2mm/aseg.mgz doug
On 10/29/2013 11:46 AM, Suzanne Oosterwijk wrote:
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 mailto:s.oosterwijk@neu.eduva.nl http://va.nl
https://sites.google.com/site/suzanneoosterwijk/
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