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:
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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 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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