Hi Hebah,
Interesting application. You could try running mri_synthstrip then analyse the
resulting binary mask to determine the first and last slices in each direction.
-Paul
________________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Hebah Tanveer
<hebah.tanv...@biotexmedical.com>
Sent: Monday, June 17, 2024 5:18 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Brain in a Box
External Email - Use Caution
I'm trying to determine the smallest rectangular prism that a brain will fit in
based on its MRI scan. My strategy is as follows: I am moving through the brain
axially, sagittally, and coronally to see where the brain "starts" appearing
and "stops" appearing. Then, I'm subtracting the amount of no-brain slices from
the total number of slices and multiplying the result by the slice thickness.
This should get me the length (sagittal plane), width (coronal plane), and
height (axial plane) of a box that contains the brain.
Is there a function within FreeSurfer that can automate this process of
determining "first and last sight of brain" ? It is quite time consuming to
manually check hundreds of patients!
Best,
Hebah
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