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"
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
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
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
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
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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
