Search found 1351 matches

by riviere
Wed Dec 09, 2020 11:52 am
Forum: BrainVISA
Topic: Morphologist - Symmetric atlas to reduce bias?
Replies: 1
Views: 1464

Re: Morphologist - Symmetric atlas to reduce bias?

Hi, In Morphologist, the segmentation part is not lateralized, and thus will process a reversed image the way you expect. If I understand this is what you see, the segmented image and extracted folds show the reversed asymmetry you were expecting. Now the sulci recognition is using an asymmetric atl...
by riviere
Wed Dec 09, 2020 11:17 am
Forum: BrainVISA
Topic: BrainVISA support and future
Replies: 3
Views: 1607

Re: BrainVISA support and future

Yes the next distribution will be VM-based, using either Singularity or VirtalBox (both will be supported, maybe docker later). It will be possible to build another image with added libraries and toolboxes, but the modular distribution as it was using the installer will be lost, because VM images do...
by riviere
Mon Nov 16, 2020 11:06 am
Forum: BrainVISA
Topic: BrainVISA support and future
Replies: 3
Views: 1607

Re: BrainVISA support and future

Hi, Brainvisa is not dead but we struggle to perform maintenance and releases. We are not many people working on it and we have difficulties to handle system compatibilities for every system / distribution. That's why we will release the next version of brainvisa as a container or (and) virtual mach...
by riviere
Mon Sep 09, 2019 2:59 pm
Forum: BrainVISA
Topic: sulci recognition error
Replies: 3
Views: 9214

Re: sulci recognition error

Hi, The energy_plot_file.nrj is a record of the global (whole hemisphere) energy across the optimization, it does not contain the local energies. I don't remember any process providing this locally. It could be done of course because they are used during the identification process, but it's not read...
by riviere
Mon Sep 09, 2019 2:53 pm
Forum: BrainVISA
Topic: Error message Brainvisa 4.5.0 Import T1 MRI
Replies: 1
Views: 4061

Re: Error message Brainvisa 4.5.0 Import T1 MRI

Hi, Well 4.5 is rather old and we cannot guarantee a maintenance on it. You can open the log window and look for the error in the process execution, it may contain more details on the command execution and its failure, but as I said, we will not fix it on 4.5. Especially if it works in 4.6 this prob...
by riviere
Mon Sep 09, 2019 2:48 pm
Forum: BrainVISA
Topic: installing Brainvisa 4.6.1 Mac error
Replies: 2
Views: 5998

Re: installing Brainvisa 4.6.1 Mac error

We have finally found why the Mac version doesn(t run on recent Macs. A part of the python package was missing. I have put a new tarball of the python package here: ftp://ftp.cea.fr/pub/dsv/anatomist/updates/4.6.1/osx/python.tar.gz It should be un-tared in the root directory of the BrainVisa install...
by riviere
Wed Aug 07, 2019 10:21 am
Forum: BrainVISA
Topic: sulci recognition error
Replies: 3
Views: 9214

Re: sulci recognition error

Hi, This old process was designed for the oldest models (ANN), and thus is using the ANN model file (not used in SPAM method) to provide a recognition energy which will not be useful to you. Anyway I think the problem is in the kind of labels the process is using: labels are stored in attributes in ...
by riviere
Tue Jul 09, 2019 3:51 pm
Forum: Anatomist
Topic: libCifti.dll missing windows 7 BrainVISA 4.6.1
Replies: 3
Views: 8697

Re: libCifti.dll missing windows 7 BrainVISA 4.6.1

Hi, Oh you are right, the libCifti didn't get into 4.6.1 distribs. We will fix that for the next one. In the meantime I have put the libs in ftp://ftp.cea.fr/pub/dsv/anatomist/updates/4.6.1/<system>/lib/ (replace <system> with win64, osx, linux64-glibc-2.23 etc). For linux there are 3 times the same...
by riviere
Tue Jun 18, 2019 11:51 am
Forum: BrainVISA
Topic: installing Brainvisa 4.6.1 Mac error
Replies: 2
Views: 5998

Re: installing Brainvisa 4.6.1 Mac error

Hi, We have been reported problems on recent Mac systems that we don't have on hand. I could observe it once but could not solve it on the fly. It seems that on some of these systems, a different python installation (the system one) gets loaded when we call the one from brainvisa, regardless of PATH...
by riviere
Thu Jun 06, 2019 1:11 am
Forum: BrainVISA
Topic: ERROR in Cingular Pole Projection 2 System call crashed
Replies: 1
Views: 4136

Re: ERROR in Cingular Pole Projection 2 System call crashed

Hi François,
A program run by the process has crashed, the log should provide more details (the exact command which was run with its parameters).

The cingular pole extraction seems to cause problems on this specific patient. Do the segmentation and meshes look OK ?
Denis
by riviere
Tue Mar 05, 2019 10:01 am
Forum: Anatomist
Topic: loading transformation with pyAnatomist
Replies: 4
Views: 6693

Re: loading transformation with pyAnatomist

In this case, the window should probably be set in the referential you consider to be Talairach (usually it's the default red one). You can assign a referential to a window just as to an object: window.assignReferential(target) It doesn't need to be the referential of an object, but there has to be ...
by riviere
Mon Mar 04, 2019 6:15 pm
Forum: BrainVISA
Topic: BrainVISA's python crashes after last Ubuntu16 upgrade
Replies: 4
Views: 6991

Re: BrainVISA's python crashes after last Ubuntu16 upgrade

OK.
Oh there is also a libpthread.so which should be removed (we'll have to check all libs next time).
Denis
by riviere
Mon Mar 04, 2019 12:14 pm
Forum: BrainVISA
Topic: BrainVISA's python crashes after last Ubuntu16 upgrade
Replies: 4
Views: 6991

Re: BrainVISA's python crashes after last Ubuntu16 upgrade

Hi, I could reproduce (more or less) the problem in a docker container (it seems a bit random, sometimes works, sometimes crashes). I guess you are using the ubuntu 16 variant of brainvisa binary distribution (glibc-2.23), right ? It appears that some libs got included in this package by accident th...
by riviere
Mon Mar 04, 2019 10:36 am
Forum: Anatomist
Topic: loading transformation with pyAnatomist
Replies: 4
Views: 6693

Re: loading transformation with pyAnatomist

Hi Olivier, If you are running this exact code, then it's normal since all objects have been assigned the same referential (source), so whatever the transformations to other referentials (target), it doesn't change anything for them. If one object (let's say aSTS) is assigned the target referential,...
by riviere
Thu Feb 07, 2019 10:36 pm
Forum: BrainVISA
Topic: Handling dimensions/transformation in Create Sulcus Label Volume Output
Replies: 1
Views: 4392

Re: Handling dimensions/transformation in Create Sulcus Label Volume Output

Hi, I haven(t checke precisely right now, but I guess the shift is due to transformations in the original image header not being copied to the sulci image. To fix this you can write a little python script using the pyaims libraries in brainvisa: from soma import aims t1_image = "path_to_t1.nii&...