Search found 1351 matches

by riviere
Mon Mar 05, 2018 10:49 am
Forum: Anatomist
Topic: How to activate coloring by normals using pyanatomist ?
Replies: 5
Views: 14200

Re: How to activate coloring by normals using pyanatomist ?

Hi, Well, actually there is a trick to setup normals colors, it's not very convenient but it should work until we do something better: # load/init anatomist import anatomist.api as ana a = ana.Anatomist() # load a mesh mesh = a.loadObject('soma_mesh.mesh') # get low-level Material object (not the sa...
by riviere
Fri Mar 02, 2018 1:42 am
Forum: Anatomist
Topic: How to activate coloring by normals using pyanatomist ?
Replies: 5
Views: 14200

Re: How to activate coloring by normals using pyanatomist ?

Hi,
Well, after checking it seems that we haven't done any python bindings for these set of functionalities... That's definitely something we could do...
Denis
by riviere
Fri Feb 23, 2018 11:06 am
Forum: BrainRAT toolbox
Topic: Bug in primatologist -> Basic Mixture Fitting
Replies: 6
Views: 15861

Re: Bug in primatologist -> Basic Mixture Fitting

Hi Olivier,
So it's an old pip. You can try to upgrade pip first, using easy_install:

Code: Select all

<brainvisa_dir>/bin/easy_install -U --prefix <brainvisa_dir> pip
then retry the pip command
Denis
by riviere
Wed Feb 21, 2018 11:55 am
Forum: BrainRAT toolbox
Topic: Bug in Primatologist -> Brain Parcellation (EM)
Replies: 12
Views: 54190

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

Hi,
Yaël has done a fix, that you can get here:
ftp://ftp.cea.fr/pub/dsv/anatomist/upda ... gist/io.py
Denis
by riviere
Tue Feb 20, 2018 5:58 pm
Forum: BrainRAT toolbox
Topic: Bug in primatologist -> Basic Mixture Fitting
Replies: 6
Views: 15861

Re: Bug in primatologist -> Basic Mixture Fitting

Can you try to upgrade directly in the brainvisa install directory ?

Code: Select all

<brainvisa_dir>/bin/pip install -U --prefix <brainvisa_dir> numpy scipy
just in case it works ;) (I haven't tried and the pip version here has problems, I had to reinstall it manually)
Denis
by riviere
Tue Feb 20, 2018 5:32 pm
Forum: BrainRAT toolbox
Topic: Bug in primatologist -> Basic Mixture Fitting
Replies: 6
Views: 15861

Re: Bug in primatologist -> Basic Mixture Fitting

Hi,
I probably forgot to upgrade numpy on this machine...
Denis
by riviere
Mon Feb 19, 2018 3:59 pm
Forum: BrainRAT toolbox
Topic: Primatologist crash due to sql problem
Replies: 2
Views: 11460

Re: Primatologist crash due to sql problem

Hi, Is the problem specific to Primatologist ? It seems to have problems using the sqlite database of Soma-Workflow, so I wonder if the soma-workflow database didn't get corrupted or something. If you are using local computing, you can exit brainvisa, and remove the file(s) $HOME/.soma-workflow/soma...
by riviere
Thu Feb 01, 2018 12:04 pm
Forum: Anatomist
Topic: Quantifying the Perimeter of an ROI/ Making Linear Measurements
Replies: 3
Views: 11672

Re: Quantifying the Perimeter of an ROI/ Making Linear Measurements

Hi, Let's answer the last question first: Also in your last example, I see that you set the ROI ID to 10, I don't think I quite understand what this is referencing. Does each brain have it's own ID? In our code our ROI ID is always 100 and since I inherited it and made changes to it to work for peri...
by riviere
Tue Jan 30, 2018 5:34 pm
Forum: AIMS
Topic: Topological correction step
Replies: 1
Views: 10425

Re: Topological correction step

Hi, Well, you might try using VipHomotopic, which is the command we are using for morphologist grey/white interface correction. Its use may be not so straightforward since we normally use it in a somewhat specific context, and I actually don't remember exactly if it has been modified out of a genera...
by riviere
Mon Jan 29, 2018 12:37 pm
Forum: Anatomist
Topic: Not same coordinates displayed into registered files
Replies: 4
Views: 13397

Re: Not same coordinates displayed into registered files

I cannot be completely sure without actually manipulating the data but I think it's actually the "snap to slice" of anatomist which disturbs you. It's just that the position of the cursor is snapped to match the (integer) slice number displayed on the slice cursor, the data and its registr...
by riviere
Mon Jan 29, 2018 10:29 am
Forum: Anatomist
Topic: Not same coordinates displayed into registered files
Replies: 4
Views: 13397

Re: Not same coordinates displayed into registered files

Hi, It seems that you forgot to attach the images :) I'm not totally sure to understand your problem then. But I have perhaps a beginning of clue: When Anatomist displays volumes, the volume slice position is snapped to the center of the slice, depending on the volume voxel size. So if you display t...
by riviere
Fri Jan 26, 2018 10:23 am
Forum: BrainVISA
Topic: morphologist -> morphometry -> brain volumes error with data imported from freesurfer
Replies: 2
Views: 12222

Re: morphologist -> morphometry -> brain volumes error with data imported from freesurfer

After checking it seems that this is just a stupid bug in an old process, which declares a parameter as an output where it is an input. So the voronoi is not overwritten as I feared. There is a patched version of the faulty process here: ftp://ftp.cea.fr/pub/dsv/anatomist/updates/4.5.0/brainvisa/too...
by riviere
Wed Jan 24, 2018 4:10 pm
Forum: BrainVISA
Topic: problem running a .bvproc from the command line
Replies: 2
Views: 12027

Re: problem running a .bvproc from the command line

Hi Sylvain, I haven't had a look at it but I may have a clue: processes run from the commandline run by default with databasing disabled. This process probably makes use of the databasing capabilities, so doesn't work when databasing is disabled. You can try it with DB forced enabled. You may use th...
by riviere
Wed Jan 24, 2018 4:00 pm
Forum: BrainVISA
Topic: morphologist -> morphometry -> brain volumes error with data imported from freesurfer
Replies: 2
Views: 12222

Re: morphologist -> morphometry -> brain volumes error with data imported from freesurfer

Hi, Whew, you're completely right: this process tries to overwrite the hemispheres spit file (voronoi) for a reason that I have not investigated yet, and appears to do it using a very old, obsolete process which is not the one used now in morphologist... So I would certainly not recommend just unloc...
by riviere
Mon Jan 15, 2018 12:37 pm
Forum: BrainVISA
Topic: libraries not loading - ubuntu 16.04
Replies: 1
Views: 11778

Re: libraries not loading - ubuntu 16.04

Hi, Which variant of Brainvisa binary distribution are you running ? The Ubuntu 12.04 variant, or the Mandriva 2008 variant ? We have found out that both have some missing thirdparty libraries which can in some cases explain several problems (libraries not loading, or conflicts). The Mandriva versio...