I'm
wondering if the bbox() implementation in Surfa (https://github.com/freesurfer/surfa/tree/master)
will achieve the task?
surfa.image.framed.bbox() (https://github.com/freesurfer/surfa/blob/master/surfa/image/framed.py#L203)
computes the bounding box of the image data greater than
zero.
I tried it on bert orig.mgz,
>>> import surfa as sf
>>>
bert='/usr/local/freesurfer/dev/subjects/bert/mri/orig.mgz'
>>> vol=sf.load_volume(bert)
>>> vol
sf.Volume(shape=(256, 256, 256), dtype=uint8)
>>> vol.shape
(256, 256, 256)
>>> bbox=vol.bbox()
>>> bbox
(slice(47, 207, None), slice(3, 255, None), slice(3, 252,
None))
Yujing
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu>
On Behalf Of Wighton, Paul
Sent: Monday, June 17, 2024 5:34 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Brain in a Box
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-bounces@nmr.mgh.harvard.edu
<freesurfer-bounces@nmr.mgh.harvard.edu>
on behalf of Hebah Tanveer <hebah.tanveer@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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