Search found 1351 matches

by riviere
Wed Aug 15, 2018 9:08 pm
Forum: BrainVISA
Topic: Holes in white matter mesh
Replies: 1
Views: 3604

Re: Holes in white matter mesh

Hi Olivier, Sorry I didn't see your post, the forum notification seems broken... Well, what you're saying is a bit frightening... If the decimation process creates holes in meshes, it's not normal at all. The algorithm hasn't been modified in decades so all meshes ever created by brainvisa might be ...
by riviere
Thu Jul 12, 2018 3:12 pm
Forum: Anatomist
Topic: RGBA palette in pyanatomist
Replies: 6
Views: 5597

Re: RGBA palette in pyanatomist

Right ;)
By the way I fixed the update bug in anatomist sources (bug_fix branch, version 4.6.1).
Denis
by riviere
Tue Jul 10, 2018 2:49 pm
Forum: BrainVISA
Topic: Errors with Sulci Recognition in Morphologist Pipeline
Replies: 2
Views: 4107

Re: Errors with Sulci Recognition in Morphologist Pipeline

Hi Will, Sorry I missed the notificatioin for your message and I had not seen it before today... Well... First the Mac version is definitely not optimal: we use an old Mac system (10.5) featuring an old compiler, an old python language version, and old libraries. We have seen that some programs run ...
by riviere
Tue Jul 10, 2018 1:59 pm
Forum: Anatomist
Topic: RGBA palette in pyanatomist
Replies: 6
Views: 5597

Re: RGBA palette in pyanatomist

Hi Guillaume, I guess what is missing is an extra parameter "texture_index=1" in the TexturingParams command: actually a Fusion2D has 2 textures, and the mixing mode you want to apply here is when merging the 2nd texture (index 1) with the previous one, thus the merging textue index is 1. ...
by riviere
Thu Jun 28, 2018 5:52 pm
Forum: BrainVISA
Topic: MRI segmentation using morphologist 2015 error
Replies: 7
Views: 6201

Re: MRI segmentation using morphologist 2015 error

It depends on he context :)
Well morphologist often outputs this kind of messages in a non-harmful way. If the process goes to the end and produces readable results, then it is OK. I admit that the messages are misleading...
Denis
by riviere
Thu Jun 28, 2018 1:28 pm
Forum: BrainVISA
Topic: MRI segmentation using morphologist 2015 error
Replies: 7
Views: 6201

Re: MRI segmentation using morphologist 2015 error

Hi,
Have you used the T1 MRI importation process before running morphologist ? Normally this process takes care of all conversions for Morphologist.
If it still desn't work, then there is a "real" problem...
Denis
by riviere
Fri Jun 08, 2018 2:52 pm
Forum: Anatomist
Topic: RGBA palette in pyanatomist
Replies: 6
Views: 5597

Re: RGBA palette in pyanatomist

Hi Guillaume, Yes normally you are right, except that... there is a bug. The transparency status of the palette is not updated when calling customPalette.setColors(...). I'm fixing this. In the meantime, you can call manually, after setColors(): customPalette.update() Note also that depending on the...
by riviere
Fri Jun 01, 2018 5:13 pm
Forum: BrainVISA
Topic: Off line install for MAC
Replies: 1
Views: 3360

Re: Off line install for MAC

Hi, Well we have a little problem on the Mac currently: the machine we are using to build has partly crashed its disk, and now it curiously fails the step where it builds the .dmg image for the installer (whereas everything else seems to still work). So it breaks all the automatic procedure for pack...
by riviere
Fri Jun 01, 2018 4:29 pm
Forum: BrainVISA
Topic: Importing T1
Replies: 1
Views: 3366

Re: Importing T1

Hi, dcm2nii is part of Mricron , it''s a tool that has to be installed seprately. However there is obviously a missing test in the import process since it should not try to use this converter if Mricron is not detected. Could you give us a bit more details about the error when using AimsFileConvert ...
by riviere
Mon May 28, 2018 6:17 pm
Forum: Anatomist
Topic: Registration issue
Replies: 3
Views: 3878

Re: Registration issue

Preferences are not saved automatically, we consider it's a deliberate user action, especially if they have been modified by a script. You can change them this way: import anatomist.api as ana a = ana.Anatomist() a.config()['setAutomaticReferential'] = 1 a.config()['commonScannerBasedReferential'] =...
by riviere
Mon May 28, 2018 1:11 pm
Forum: Anatomist
Topic: Registration issue
Replies: 3
Views: 3878

Re: Registration issue

Hi, Welcome to the amazing world of coordinates transformations :) If you go in Anatomist preferences, "volumes" tab, and check both options "use referential/transformation information from header" and "assume all 'scanner-based' referentials are the same", then load th...
by riviere
Mon May 21, 2018 10:34 pm
Forum: BrainVISA
Topic: Calling "Import FreeSurfer grey/white segmentation to Morphologist" from a script
Replies: 2
Views: 3724

Re: Calling "Import FreeSurfer grey/white segmentation to Morphologist" from a script

Hi, It should normally work as you had expected but it may behave differently if databases have been disabled at startup in your script. As I don't know how it starts, I cannot really tell... If databases are enabled and setup (you need a Freesurfer database and a Morphologist database for the proce...
by riviere
Mon May 07, 2018 11:53 am
Forum: BrainVISA
Topic: Compilation Error: Ubuntu 16.04 LTS
Replies: 2
Views: 3976

Re: Compilation Error: Ubuntu 16.04 LTS

Hi Alex, There seems to be a problem with the Minc lib configurartion: it is detected (since it tries to compile the minc module) but the headers location is not correct. Can you try moving away the CMakeCache.txt file in the root build directory, and try again doing bv_maker configure build ? If th...
by riviere
Mon Apr 30, 2018 5:59 pm
Forum: BrainVISA
Topic: Database is locked
Replies: 2
Views: 3785

Re: Database is locked

Hi, BrainVisa is using SQlite to manage its databases. SQLite works without a server, and uses a file locking mechanism to avoid concurrent access to the database. However this locking mechanism is provided by the filesystem, and it appears that NFS does not implement it correctly (NFS3 at least). W...
by riviere
Sun Apr 29, 2018 8:21 pm
Forum: Anatomist
Topic: QPixmap::setMask() mask size differs from pixmap size
Replies: 17
Views: 10835

Re: QPixmap::setMask() mask size differs from pixmap size

Hi, There is certainly a way, but it's very difficult to help you since we cannot reproduce the problem, and it doesn't seem to happen outside of your specific script using Intranat, so the only thing I can do is guess and imagine potential explanations... I suppose Intranat is not making use of thr...