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
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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Begüm Cerrahoğlu cerrahoglubegum@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: msg18797https://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
External Email - Use Caution
Hi Andrew,
Thank you greatly for your quick response. In the process of implementing your solution, I came across another issue and hope that you could help me solve it.
I went ahead and ran the SynthStrip script using singularity. This gave me newly stripped T1 and brainmask files. However, when I tried to run recon-all again, using these files, it exited with errors saying white matter peak found at 0 -I tried recon-all by replacing the existing T1 and brainmask files from the mri folder of sub-02 and running recon-all using the -make flag. Should I have tried to recon from the beginning using only the T1 file?
Below you can find the error I got in the normalization step:
#@# Intensity Normalization2 Fri Mar 18 20:34:47 CET 2022 /home/inekepillet/Downloads/freesurfer/sub-02/mri
mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz
assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... Reading aseg aseg.presurf.mgz normalizing image... processing with aseg removing outliers in the aseg WM... 0 control points removed Building bias image building Voronoi diagram... performing soap bubble smoothing, sigma = 0... Smoothing with sigma 8 Applying bias correction HISTOalloc(-2147483648): could not allocate histogram building Voronoi diagram... performing soap bubble smoothing, sigma = 8...
Iterating 2 times --------------------------------- 3d normalization pass 1 of 2 white matter peak found at 0 Cannot allocate memory
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.
All the best,
Begum Cerrahoglu
Hoopes, Andrew AHOOPES@mgh.harvard.edu, 16 Mar 2022 Çar, 15:34 tarihinde şunu yazdı:
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-bounces@nmr.mgh.harvard.edu < freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Begüm Cerrahoğlu < cerrahoglubegum@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 ofgm and cerebellum for over-aggressive cutting.Add -segmentation brainmask.gcuts.mgz to the tkmeditcommand 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 "
FreeSurfer version: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.
Platform: Linux Mint 20.2
Thank you greatly for your time and efforts.
Kindest regards,
Begum Cerrahoglu
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Begüm Cerrahoğlu -
Hoopes, Andrew