Re: [Freesurfer] SAMSEG - hanging for FLAIR lesion segmentation

External Email - Use Caution

Hi Stefan,

Thanks for the response.

PFA the log.

Here is one frame of registration.

[image: image.png]

Thanks and regards, Sravanthi.

On Fri, Sep 6, 2024 at 12:47 PM Stefano Cerri stce@di.ku.dk wrote:

Hi Sravanthi,

Can you check that "template_coreg.mgz" produced by samseg is aligned with your FLAIR image? There might be an issue with the initial template registration. If that is not the case, can you provide the full SAMSEG log? A warning might have been issued before it hung there.

Stefano

[Freesurfer] SAMSEG - hanging for FLAIR lesion segmentation https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22%5C%5BFreesurfer%5C%5D+SAMSEG+%5C-+hanging+for+FLAIR+lesion+segmentation%22&o=newest

Sravanthi Upadrasta https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Sravanthi+Upadrasta%22 Thu, 05 Sep 2024 04:46:51 -0700 https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20240905

    External Email - Use Caution

Hi,

I am encountering an issue with Samseg while extracting lesion information from a CUBE FLAIR image. The process hangs for a long time and I have to forcekill the process after almost 2 hours. I did not have this issue with same subject T1w and T2 FLAIR images. Freesurfer - 7.2.0 Ubuntu 20.04

Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz Transforming points Transforming points Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz Read mesh collection: /usr/local/freesurfer/7.2.0/average/samseg/20Subjects_smoothing2_down2_smoothingForAffine2_lesion/atlas_level2.txt.gz

Could you help me troubleshoot this?

Thanks, Sravanthi.

---

Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline https://www.massgeneralbrigham.org/complianceline . 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 receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.