Search found 5 matches

by yael
Fri Jun 29, 2018 9:29 am
Forum: BrainRAT toolbox
Topic: Bug in Primatologist -> Brain Parcellation (EM)
Replies: 12
Views: 10633

Re: Bug in Primatologist -> Brain Parcellation (EM)

Hi Olivier, It took me even more time to answer, but the bug is finally fixed! I also found another bug in the skull-stripping process: in T1, it selected as "brain component" components that I actually wanted to discard. It seems to work a lot better now (at least on your image). Those tw...
by yael
Mon Mar 05, 2018 3:25 pm
Forum: BrainRAT toolbox
Topic: Bug in Primatologist -> Brain Parcellation (EM)
Replies: 12
Views: 10633

Re: Bug in Primatologist -> Brain Parcellation (EM)

Hi Olivier,

I finally have an up-to-date Brainvisa :)
I couldn't reproduce this issue with my test data. Do you think you could give me access to tour input MRI (and maybe the resulting affine and FFD transforms) so that I test in on my machine?

Thanks a lot for your help

Yaël
by yael
Fri Feb 23, 2018 1:07 pm
Forum: BrainRAT toolbox
Topic: Bug in Primatologist -> Brain Parcellation (EM)
Replies: 12
Views: 10633

Re: Bug in Primatologist -> Brain Parcellation (EM)

I think it comes from the resampling. I'll try to reproduce the issue and let you know.
If I can't manage to reproduce it, I might need some help from you, if you don't mind (like access to the affine and FFD transforms)

Yaël
by yael
Thu Feb 22, 2018 11:39 pm
Forum: BrainRAT toolbox
Topic: Bug in Primatologist -> Brain Parcellation (EM)
Replies: 12
Views: 10633

Re: Bug in Primatologist -> Brain Parcellation (EM)

Hi Olivier, I was going to blame the skull-stripping, which is the most unstable step of the pipeline, but it doesn't seem to have this cut (even though it keeps way too much tissue around the brain, there's room for improvement). Could you post screenshots of the affine and nonlinear registration s...
by yael
Tue Feb 20, 2018 6:44 pm
Forum: BrainRAT toolbox
Topic: Bug in Primatologist -> Brain Parcellation (EM)
Replies: 12
Views: 10633

Re: Bug in Primatologist -> Brain Parcellation (EM)

Hi Olivier, It seems that the read voxel size does not contain 4 values, as expected. It never happened before with me, but I obviously only used a limited range of images/formats. Could you apply aimsFileInfo (which is in brainvisa.data.neuroDiskItems) to your input file, in ipython and tell me if ...

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