Re: [Freesurfer] Help with samseg

[fsbuild]

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If you are working on a silicon (not Intel) Mac with an M1, M2, M3 processor, 
then try downloading and installing the development build of freesurfer for the 
silicon 
Mac,https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/freesurfer-macOS-darwin_arm64-dev.pkgNow
 you may not get the same numerical results with this newer 2024 build compared 
to the 7.3.2 release from 2022, but you will get any/all the latest 
updates/fixes with the 2024 build.
- R.
On Aug 30, 2024, at 19:20, Cacciaguerra, Laura, M.D., Ph.D. 
 
wrote:External Email - Use 
CautionHello everyone,I am 
trying to segment MS lesions with "samseg" (FreeSurfer version 7.3.2), but it 
ends immediately with the following error:
"zsh: illegal hardware instruction  run_samseg --input T1.nii --input 
T2.nii  --lesion"
Have tried to run the command without the option --lesion and it works, so I 
guess the error is somehow linked to that option?
Thank you in advance for your help,All the 
best,Laura___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] Help with samseg

[Cacciaguerra, Laura, M.D., Ph.D.]

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Hello everyone,
I am trying to segment MS lesions with "samseg" (FreeSurfer version 7.3.2), but 
it ends immediately with the following error:

"zsh: illegal hardware instruction  run_samseg --input T1.nii --input T2.nii  
--lesion"

Have tried to run the command without the option --lesion and it works, so I 
guess the error is somehow linked to that option?

Thank you in advance for your help,
All the best,
Laura
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addressed.  If you believe this e-mail was sent to you in error and the e-mail 
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 .
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Re: [Freesurfer] help with SAMSEG

[Hoopes, Andrew]

The atlases used by samseg are very different from freesurfer GCAs, and the 
samseg-template creation is not an easily-accessible utility at the moment. 
Feel free to look through the GEMS code in the FS repository, but it might be 
some time before we have an easy-to-use samseg atlas building tool in 
freesurfer.

Best
Andrew

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alberto Del Cerro Leon 

Date: Wednesday, May 5, 2021 at 11:11 AM
To: Freesurfer support list 
Subject: [Freesurfer] help with SAMSEG

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Hello Freesurfer team, my group is interested in using the SAMSEG tool to 
evaluate white matter lesions in MCI patients. We would like to use a 
personalized atlas for the measure. We suppose that we need to use the flag 
--atlas but we don`t know if we need a generic atlas or we need an atlas at 
each subject' spaces.

Thanks in advance for your help.
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the e-mail was sent to you in error but does not contain patient information, 
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[Freesurfer] help with SAMSEG

[Alberto Del Cerro Leon]

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Hello Freesurfer team, my group is interested in using the SAMSEG tool to
evaluate white matter lesions in MCI patients. We would like to use a
personalized atlas for the measure. We suppose that we need to use the flag
--atlas but we don`t know if we need a generic atlas or we need an atlas at
each subject' spaces.

Thanks in advance for your help.
___
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