Re: [Freesurfer] Ex-vivo adult brain MRI segmentation and surface analysis

[Douglas N. Greve]

That does not look like it is a problem with the input image. Do you 
have a normal, invivo MRI that you can run samseg on to see if it is 
just a problem with your platform?


On 1/18/2024 3:57 AM, K Eswar wrote:


External Email - Use Caution

Dear FS community

I have an ex-vivo human adult brain MRI, both in T1 MPRAGE and Fiesta. 
I have recently come across a paper on MRI segmentation using a 
function called- samseg. From the webpage( *MailScanner has detected a 
possible fraud attempt from "secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/ExvivoRecon 
) 
I realized that there is a different approach altogether to processing 
these fixative brains. However, as a first step, when I tried the 
samseg function, I noticed that the function exited with errors.


The steps where it fails are:
Read mesh collection: 
/home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz

Transforming points
Transforming points
Read mesh collection: 
/home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
Read mesh collection: 
/home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz

Killed

I am using the Ubuntu 22.04 version with RAM 32GB
Freesurver version: 
freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275


I would greatly appreciate it if you could help me with MRI 
segmentation and cortical surface analysis on these brains.


Thanks for your time and consideration.

Regards
K Eswar
Project Scientist
Sudha Gopalakrishnan Brain Centre
IIT Madras, India

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[Freesurfer] Ex-vivo adult brain MRI segmentation and surface analysis

[K Eswar]

External Email - Use Caution

Dear FS community

I have an ex-vivo human adult brain MRI, both in T1 MPRAGE and Fiesta. I
have recently come across a paper on MRI segmentation using a function
called- samseg. From the webpage(
https://secure-web.cisco.com/1AJdw_iZ93Ctl2bXUM-tS9sQoJ_9a6-0RHBNEGqz7c8Pz8GSVQSAS9NvPicCtOfOlcCk2usfSQaphR2x5O9OtMVeO3byxBTtWanL1Lo6pkUBbO7WBqlr0s2GXTavc8OsJmxaGyjxPXbpYGjyC-R9lbgqfpPqvPSFBqUm2C1CcpmZtpG68WfRTj09GXjjGFDeJvf9e1rMz7DTEq_IjhzeX_ueSNnY8PVK6WlzPVLcJT-wzuUaplRF9gMRJevnnNwDO9_ahhh74NOapQ6VO_0eaM8Vbsa9FN4_n6ghVPXg-ptwtkfgZtPfaTd8CDM1lEKjcGz9EsuNtBKF8XpvLnJQS3g/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FExvivoRecon)
 I realized that
there is a different approach altogether to processing these fixative
brains. However, as a first step, when I tried the samseg function, I
noticed that the function exited with errors.

The steps where it fails are:
Read mesh collection:
/home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
Transforming points
Transforming points
Read mesh collection:
/home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
Read mesh collection:
/home/sgbc/freesurfer/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2/atlas_level2.txt.gz
Killed

I am using the Ubuntu 22.04 version with RAM 32GB
Freesurver version: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275

I would greatly appreciate it if you could help me with MRI segmentation
and cortical surface analysis on these brains.

Thanks for your time and consideration.

Regards
K Eswar
Project Scientist
Sudha Gopalakrishnan Brain Centre
IIT Madras, India
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Freesurfer@nmr.mgh.harvard.edu
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
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continue to communicate over unencrypted e-mail.