Hi Begum,
You could try the just-recently released SynthStrip command `mri_synthstrip`
available in the dev distributions of freesurfer (as of today, march 15th). It
should be more robust than the watershed utility.
Best,
Andrew
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Begüm Cerrahoğlu
<cerrahoglube...@gmail.com>
Date: Tuesday, March 15, 2022 at 5:26 AM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Gcut error: gcutted brain is much smaller than the mask
External Email - Use Caution
Dear developers,
I am trying to clean up the extra dura left after skullstripping. Watershed
parameter does not prove to be much helpful and when I try gcut I get the error
below.
I checked the release notes of freesurfer 5.1 and mri_gcut is not run by
default. In the archives I came across this exact problem before, under this
message:
msg18797<https://secure-web.cisco.com/1Gix4yHAghaLSVAVD-cOy4QmehGJB3UyVkUd5GwVNmFNq_g5qLr5aMQrJYjCrBpwNFyTI00KfK8fNX5mZRJWBiE9YkNRqFUkMQ-hb6YrIbDiEbal4uO2_k6OOElO4DldAZto5qT0fl7r2g4qLCaDM-Tk_U19vLbGJArE1o3LbUW-MRZexY76mCIVhkgbVKGHgNmMJ8Cx8jg4AfTAN2jxqs3nAK86niRIsjpx6wO7WH3vQakoJKKUspSEXQATjjUo7wJuH_VsuHrMXvcqk7te-fYF9b1vF_ZBzVaNPBOAb-7AwAbGCGljwWRzSgyCPbbdhIrnPgWYYEJbCc4k39bujPg/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg18797.html>
However, there was not an end solution available in the archived email exchange.
I am not interested in cerebellum and am okay with cutting the cerebellum out
of the brain mask as long as it does not interfere with being able to
distinctly separate cortex from cerebellum in the following steps.
>From skullstripping tutorials,I have read that one should not start erasing
>cerebellum from the brainmask directly and was wondering if you could let me
>know why?
In sum, are there important reasons to keep the cerebellum despite only being
interested in analyzing the cortex?
If not, could you please let me know what could be the reason for gcut's
failure and if there is anyway to disable failure detection so I can see if the
gcutted
brain is usable?
>> " rm -f brainmask.gcuts.mgz
>> mri_gcut -110 -mult brainmask.auto.mgz T1.mgz brainmask.auto.mgz
>> brainmask.gcuts.mgz
>>
>> INFO: Care must be taken to thoroughly inspect your data
>> when using mri_gcut. In particular, inspect the edges of
>> gm and cerebellum for over-aggressive cutting.
>> Add -segmentation brainmask.gcuts.mgz to the tkmedit
>> command string to view the voxels which gcut has removed.
>>
>> reading mask...
>> white mean: 107.529232
>> threshold set to: 107.529232*0.400000=43.011693
>> calculating weights...
>> doing mincut...
>> now doing maxflow, be patient...
>> g-cut done!
>> post-processing...
>> post-processing done!
>> masking...
>> ** Gcutted brain is much smaller than the mask!
>> ** Using the mask as the output instead!
>>
>> cp brainmask.auto.mgz brainmask.mgz "
1) FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.
2) Platform: Linux Mint 20.2
Thank you greatly for your time and efforts.
Kindest regards,
Begum Cerrahoglu
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