Search found 1351 matches
- Wed Aug 15, 2018 9:08 pm
- Forum: BrainVISA
- Topic: Holes in white matter mesh
- Replies: 1
- Views: 13634
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 ...
- Thu Jul 12, 2018 3:12 pm
- Forum: Anatomist
- Topic: RGBA palette in pyanatomist
- Replies: 6
- Views: 17193
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 the way I fixed the update bug in anatomist sources (bug_fix branch, version 4.6.1).
Denis
- Tue Jul 10, 2018 2:49 pm
- Forum: BrainVISA
- Topic: Errors with Sulci Recognition in Morphologist Pipeline
- Replies: 2
- Views: 14674
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 ...
- Tue Jul 10, 2018 1:59 pm
- Forum: Anatomist
- Topic: RGBA palette in pyanatomist
- Replies: 6
- Views: 17193
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. ...
- Thu Jun 28, 2018 5:52 pm
- Forum: BrainVISA
- Topic: MRI segmentation using morphologist 2015 error
- Replies: 7
- Views: 19638
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
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
- Thu Jun 28, 2018 1:28 pm
- Forum: BrainVISA
- Topic: MRI segmentation using morphologist 2015 error
- Replies: 7
- Views: 19638
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
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
- Fri Jun 08, 2018 2:52 pm
- Forum: Anatomist
- Topic: RGBA palette in pyanatomist
- Replies: 6
- Views: 17193
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...
- Fri Jun 01, 2018 5:13 pm
- Forum: BrainVISA
- Topic: Off line install for MAC
- Replies: 1
- Views: 13121
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...
- Fri Jun 01, 2018 4:29 pm
- Forum: BrainVISA
- Topic: Importing T1
- Replies: 1
- Views: 13153
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 ...
- Mon May 28, 2018 6:17 pm
- Forum: Anatomist
- Topic: Registration issue
- Replies: 3
- Views: 13540
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'] =...
- Mon May 28, 2018 1:11 pm
- Forum: Anatomist
- Topic: Registration issue
- Replies: 3
- Views: 13540
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...
- Mon May 21, 2018 10:34 pm
- Forum: BrainVISA
- Topic: Calling "Import FreeSurfer grey/white segmentation to Morphologist" from a script
- Replies: 2
- Views: 13945
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...
- Mon May 07, 2018 11:53 am
- Forum: BrainVISA
- Topic: Compilation Error: Ubuntu 16.04 LTS
- Replies: 2
- Views: 14370
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...
- Mon Apr 30, 2018 5:59 pm
- Forum: BrainVISA
- Topic: Database is locked
- Replies: 2
- Views: 13945
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...
- Sun Apr 29, 2018 8:21 pm
- Forum: Anatomist
- Topic: QPixmap::setMask() mask size differs from pixmap size
- Replies: 17
- Views: 31465
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...