[Freesurfer] WMH-SynthSeg vs. SAMSEG for WM lesions

External Email - Use Caution Hi, For SAMSEG: Are you using the --lesion-mask-pattern flag with the value "1" on the FLAIR scan? You can try to relax the masking by excluding darker than WM mean intensities voxels rather than darker than GM ones, i.e., by adding to your command:

Re: [Freesurfer] WMH-SynthSeg vs. SAMSEG for WM lesions

External Email - Use Caution Hi Stefano, For samseg isn't there also an option to disable the VAE shape model? I forgot the details, but if false positives are not an issue maybe that could also help? Koen On Friday, January 5, 2024, Stefano Cerri wrote: > External

[Freesurfer] problem with using freeview to load flattened patches

Dear Surfers, I am using freesurfer 7.1.1 to view flattened patches and I have faced two issues: 1) When I elevate the camera (see the command below), the loaded image is not centered. Is there any command (key) to recenter the image other than manually moving it? 2) The

Re: [Freesurfer] WMH-SynthSeg vs. SAMSEG for WM lesions

External Email - Use Caution I've just exposed the option to the user. It might take some days before it will be available in the development version. @sudeepti: In the new development version, if you add to your samseg command the following flag "--do-not-use-shape-model", the

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

External Email - Use Caution Thanks, but the issue isn't that graphics aren't displaying, it's that freeview won't load because qt can't be initialized. Abeoseh Flemister From: fsbuild Sent: Friday, January 5, 2024 8:27 PM To:

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

External Email - Use Caution Hi Yujing, Thanks that helped! I was trying to open freeview by typing "freeview" and I’ve unfortunately run into another error: This application failed to start because no Qt platform plugin could be initialized. I saw an

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

External Email - Use Caution For issues with Freeview displaying graphics when running via Linux on a Windows host thru WSL, you could look at the recent thread with the subject "Re: [Freesurfer] Freeview not showing output",

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

External Email - Use Caution Did you install Freesurfer 7.4.1 using the Debian installer package

[Freesurfer] recon-all vs. recon-all-clinical: missing ROIs

External Email - Use Caution Hi, recon-all generates these volumes, amongst others: "Left-vessel", "Left-choroid-plexus", "Right-vessel", "Right-choroid-plexus" recon-all-clinical does not generate these volumes. Or at least that I am able to detect. Any ideas how to extract or

[Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

External Email - Use Caution Hi FreeSurfer Team, I am attempting to run recon-all on a 3T MRI image dataset. I used recon-all \ -all \ -i 3D_T1_MPRAGE_PRE_MPR_AX.nii.gz \ -s SiroSTC006_pre and recon-all failed before completeing even the first step. I tried other files from our

[Freesurfer] modify intensity normalization pipeline

External Email - Use Caution Hello, Is there a way to modify intensity normalization pipeline in recon-all script? The temporal lobe is being very poorly segmented because white matter is being segmented as gray matter and therefore gray matter does not reach outer boundary of

[Freesurfer] poor inferior cerebellum segmentation

External Email - Use Caution Hello, Inferior portion of cerebellum are not segmented well. It is included in skullstrip and I tried adding control points in cerebellar WM but this did not help. I am not interested in cerebellum but I do need eTIV. Will this poor cerebellar

Re: [Freesurfer] recon-all -s SiroSTC006_pre exited with ERRORS

This is from your recon-all.log " mri_convert /home/abeoseh/Downloads/OneDrive_1_1-4-2024/Subject 6/Baseline/3D_T1_MPRAGE_PRE_MPR_AX.nii.gz /usr/local/freesurfer/subjects/SiroSTC006_pre/mri/orig/001.mgz mri_convert: extra argument

Re: [Freesurfer] mri_error_no_clear_message

External Email - Use Caution Hi Fargol,I recently heard about some problems from my coworkers who were using Ubuntu 18 and version 7.2.0 of the software. However, I am currently using version 7.2.0 on Ubuntu 22.04.2 LTS, and it works well for me. You could try it out and see if