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by Olivier Coulon
Tue Mar 05, 2019 5:21 pm
Forum: Anatomist
Topic: loading transformation with pyAnatomist
Replies: 4
Views: 3875

Re: loading transformation with pyAnatomist

It works, thank you very much.

Olivier
by Olivier Coulon
Tue Mar 05, 2019 9:04 am
Forum: Anatomist
Topic: loading transformation with pyAnatomist
Replies: 4
Views: 3875

Re: loading transformation with pyAnatomist

Thank you, So basically what I want to do is not to transform one object into another one's referential, but instead display several objects in the Talairach-ACPC referential. I guess it just means that I need to specify that the window should be also in thtat referential ? (if so, how ?). Olivier
by Olivier Coulon
Tue Feb 26, 2019 7:36 pm
Forum: Anatomist
Topic: loading transformation with pyAnatomist
Replies: 4
Views: 3875

loading transformation with pyAnatomist

Hello, I am trying to display a set of volumes and meshes (from the same original T1 image) in the Talairach-ACPC referential within a python script, using pyAnatomist. I used the online documentation: http://brainvisa.info/pyanatomist-4.6/sphinx/pyanatomist_tutorial_nb.html#Load-a-transformation an...
by Olivier Coulon
Wed Jul 25, 2018 4:57 pm
Forum: BrainVISA
Topic: Holes in white matter mesh
Replies: 1
Views: 2488

Holes in white matter mesh

Hello, this post is just to point out something I noticed while importing unusual data, i.e. chimpanzee data that have been segmented with a different software. I imported segmentations into BV, ran the missing step, etc... Then I ran the topological corrections, then the grey/white mesh extraction....
by Olivier Coulon
Wed Mar 28, 2018 3:18 pm
Forum: BrainRAT toolbox
Topic: Bug in Primatologist -> Brain Parcellation (EM)
Replies: 12
Views: 12950

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

Hello Yaël,
sorry for the time it took to answer. I reproduced the problem on another subject. You can download the entire subject's directory following this link:

https://cloud.int.univ-amu.fr/index.php/s/k23DGYSy7DEgQXA

Let me know if I can help.

Olivier
by Olivier Coulon
Fri Feb 23, 2018 2:10 pm
Forum: BrainRAT toolbox
Topic: Bug in Primatologist -> Brain Parcellation (EM)
Replies: 12
Views: 12950

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

Of course, let me know how I can help.
Thanks.

Olivier
by Olivier Coulon
Fri Feb 23, 2018 10:12 am
Forum: BrainRAT toolbox
Topic: Bug in Primatologist -> Brain Parcellation (EM)
Replies: 12
Views: 12950

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

Here it is, affine on the left, non linear on the right.
https://www.dropbox.com/s/1026o4ltxlylty0/affine_nonlinear.jpg?dl=0

It actually stops at a specific slice, like if it was forced too.


Olivier
by Olivier Coulon
Thu Feb 22, 2018 8:14 am
Forum: BrainRAT toolbox
Topic: Bug in Primatologist -> Brain Parcellation (EM)
Replies: 12
Views: 12950

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

Hello Yaël, I managed to run the entire pipeline on two different T1 macaque images. On one of them, there is a problem that you can see on the snapshot below: https://www.dropbox.com/s/htqie5zwvhvz2w7/primatologist.jpg?dl=0 The brain mask is cut at the top and part of the brain is excluded. I tried...
by Olivier Coulon
Thu Feb 22, 2018 8:00 am
Forum: BrainRAT toolbox
Topic: Bug in primatologist -> Basic Mixture Fitting
Replies: 6
Views: 3663

Re: Bug in primatologist -> Basic Mixture Fitting

Hello Denis,
pip install does not have any --prefix option.

Olivier
by Olivier Coulon
Wed Feb 21, 2018 11:59 am
Forum: BrainRAT toolbox
Topic: Bug in Primatologist -> Brain Parcellation (EM)
Replies: 12
Views: 12950

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

Thank you ! I tried a simple fix myself already and it worked.
I will use yours and let you know.

Olivier
by Olivier Coulon
Wed Feb 21, 2018 9:20 am
Forum: BrainRAT toolbox
Topic: Bug in Primatologist -> Brain Parcellation (EM)
Replies: 12
Views: 12950

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

Hello Yaël,
indeed, eventhough the dimensions contain 4 fields (with the last one of size 1), there are only 3 values for voxel size:


'volume_dimension': [224, 336, 448, 1],
'voxel_size': [0.399993896484375, 0.40179443359375, 0.40179443359375],


I guess this is easy to fix...

Olivier
by Olivier Coulon
Tue Feb 20, 2018 6:34 pm
Forum: BrainRAT toolbox
Topic: Bug in primatologist -> Basic Mixture Fitting
Replies: 6
Views: 3663

Re: Bug in primatologist -> Basic Mixture Fitting

OK, I'll try tomorrow and will let you know.

Olivier
by Olivier Coulon
Tue Feb 20, 2018 3:48 pm
Forum: BrainRAT toolbox
Topic: Bug in Primatologist -> Brain Parcellation (EM)
Replies: 12
Views: 12950

Bug in Primatologist -> Brain Parcellation (EM)

Hello, moving on with the Primatologist pipeline, I encountered a new bug in the Bayesian Segmentation -> Brain Parcellation (EM) process: list index out of range IndexError processes.py (3174) in _processExecution: result = process.execution(self) primate_Parcellation.py (429) in execution: '-ov', ...
by Olivier Coulon
Tue Feb 20, 2018 3:43 pm
Forum: BrainRAT toolbox
Topic: Bug in primatologist -> Basic Mixture Fitting
Replies: 6
Views: 3663

Re: Bug in primatologist -> Basic Mixture Fitting

About this bug. On my debian system, we installed the Mandriva 2008 version, and it comes with a newer numpy version, so the bug is not there. On my Ubuntu, I had installed the Ubuntu 12.04 version...
by Olivier Coulon
Mon Feb 19, 2018 5:05 pm
Forum: BrainRAT toolbox
Topic: Bug in primatologist -> Basic Mixture Fitting
Replies: 6
Views: 3663

Bug in primatologist -> Basic Mixture Fitting

Hello, Moving on with Primatologist, I encountered the following bug in the "Basic Mixture Fitting" sub-process. It crashes because on lines 73, 84, 106, and 116 there is a call for the function numpy.random.choice(). This function is available in numpy from version 1.7 and above, and Brai...

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