[Freesurfer] [FreeSurfer] ValueError axes don't match array

External Email - Use Caution Hi Krystal, Can you send your samseg command and the output of mri_info on both the T1 and coregistered FLAIR images? It seems that the two images have different image sizes. Stefano Subject:[Freesurfer] [FreeSurfer] ValueError axes don't m

Re: [Freesurfer] Longitudinal SAMSEG with multi-contrast data

External Email - Use Caution Hi Gonzalo, Assuming that you have run mri_robust_template and obtained longitudinally registered images (e.g., tp0_t1_reg.mgz, tp1_t1_reg.mgz, etc...), then you can co-register each additional contrast of each time point with the commands: mri_core

[Freesurfer] R: Samseg lesion mask holes

an of the WM class (default is GM), e.g.: --lesion-mask-structure White --lesion-mask-pattern 1 However, these changes might increase false positive lesions. Stefano Da: Evie Neylon Inviato: venerdì 31 marzo 2023 04:28 A: Cerri, Stefano,PHD Cc: frees

Re: [Freesurfer] Samseg lesion mask holes

Hi Evie, --save-probabilities and --save-posteriors will save two different things for lesions. The former is an initialization of lesions based on intensity and location constraints, and the latter is a probability map of seg.mgz after we also introduce lesion shape constraints (Cf Fig.4 of h

Re: [Freesurfer] SAMSEG in MS terminal error

Hi Gabriel, These messages look like TensorFlow warnings. They just mean that you're running it on a system without GPUs. They should not stop the run. Is this the last message printed by run_samseg, or does the algorithm continues? Can you provide more details on when the run terminates? Stef

Re: [Freesurfer] Samseg cortex parcellation

Hi Valentin, Glad to hear that. Did you use the command "samseg" with the --recon flag? If yes, there are a couple of flags that you can add so that the output of SAMSEG ("seg.mgz") is used in more steps in the recon-all stream: " --fill : use samseg to create filled.mgz instead of recon-all"