Ginkgo merge requestshttps://framagit.org/cpoupon/gkg/-/merge_requests2023-09-05T13:10:11Zhttps://framagit.org/cpoupon/gkg/-/merge_requests/31texture map partial binary read2023-09-05T13:10:11ZSimon Legeaytexture map partial binary readhttps://framagit.org/cpoupon/gkg/-/merge_requests/30Fixes for VFA SPGR2023-03-22T16:36:13ZYann LeprinceFixes for VFA SPGRhttps://framagit.org/cpoupon/gkg/-/merge_requests/29add diffeomorphic_and_linear parameters2023-03-22T16:49:43ZSimon Legeayadd diffeomorphic_and_linear parametershttps://framagit.org/cpoupon/gkg/-/merge_requests/28add a mask in GkgAntsBiasFieldCorrection2023-02-20T16:29:04ZSimon Legeayadd a mask in GkgAntsBiasFieldCorrectionIvy UszynskiIvy Uszynskihttps://framagit.org/cpoupon/gkg/-/merge_requests/27increment bug fixed2022-11-10T09:27:20ZSimon Legeayincrement bug fixedIl manquait simplement un incrément qqpartIl manquait simplement un incrément qqparthttps://framagit.org/cpoupon/gkg/-/merge_requests/26Verbose issue2022-11-16T14:53:34ZBrulléVerbose issueIssues in files printing message out of verbose and impacting use of DWITensor and DWIODF functors.Issues in files printing message out of verbose and impacting use of DWITensor and DWIODF functors.https://framagit.org/cpoupon/gkg/-/merge_requests/25Modify the suffix of rotated and noise mri signature output directory name path2022-10-12T13:13:01ZBrulléModify the suffix of rotated and noise mri signature output directory name pathJ'ai changé le nom des dossiers de sorties après application des rotations et des bruits.
Originellement il y avait des "001,002,003 etc ... maintenant ça fais plutôt "RotationNumber_1 RotationNumber_2 etc..." c'est plus lisible pour mes...J'ai changé le nom des dossiers de sorties après application des rotations et des bruits.
Originellement il y avait des "001,002,003 etc ... maintenant ça fais plutôt "RotationNumber_1 RotationNumber_2 etc..." c'est plus lisible pour mes pipelines pythons.https://framagit.org/cpoupon/gkg/-/merge_requests/24correction of b1 scaling and a minor not mpi initialized anatomist plugin2022-10-06T09:43:49ZSimon Legeaycorrection of b1 scaling and a minor not mpi initialized anatomist pluginCyril PouponCyril Pouponhttps://framagit.org/cpoupon/gkg/-/merge_requests/23Revert "Filling the ellipsoid methods and a bit of refactoring"2022-09-08T10:44:02ZAnasRevert "Filling the ellipsoid methods and a bit of refactoring"Filling Ellipsoid methods in EllipsoidAtom.h and EllipsoidAtom.cxx files.
The refactoring part refers to the use of static methods, i.e get ellipsoid parameters,
these static methods are used in diffusion code and also called inside elli...Filling Ellipsoid methods in EllipsoidAtom.h and EllipsoidAtom.cxx files.
The refactoring part refers to the use of static methods, i.e get ellipsoid parameters,
these static methods are used in diffusion code and also called inside ellipsoid class methods.
Compiling code.
This reverts commit 625b50ede6755ee8f8c4afba93c513bd300a8b1d.Cyril PouponCyril Pouponhttps://framagit.org/cpoupon/gkg/-/merge_requests/22global tracto directory added2022-04-28T12:04:36ZSimon Legeayglobal tracto directory addedhttps://framagit.org/cpoupon/gkg/-/merge_requests/21Pli dmri global tractography2022-04-28T12:00:31ZSimon LegeayPli dmri global tractographyhttps://framagit.org/cpoupon/gkg/-/merge_requests/20Extraction method on cartesian field2022-04-25T17:20:24ZSimon LegeayExtraction method on cartesian fieldCyril PouponCyril Pouponhttps://framagit.org/cpoupon/gkg/-/merge_requests/19Removing from previous Fiber.cxx the method "add tortuosity" because it is...2022-04-25T13:39:59ZBrulléRemoving from previous Fiber.cxx the method "add tortuosity" because it is...Adding the tortuosity is now done in " Fiber Population " and parallelized.
For large simulation, after experimentation, the time dedicated to the tortuosity formation is exponentially improved, but for small simulation the classic way c...Adding the tortuosity is now done in " Fiber Population " and parallelized.
For large simulation, after experimentation, the time dedicated to the tortuosity formation is exponentially improved, but for small simulation the classic way can be better.
If this upgrade is merge we can parallelize tortuosity for glial cells aswell.https://framagit.org/cpoupon/gkg/-/merge_requests/18Minor fixes: eigenvalue test condition and last parameter value2022-04-14T12:37:36ZAnasMinor fixes: eigenvalue test condition and last parameter value- Changing the test condition for the ellipsoidMatrix eigenvalues (if one of the eigvalues is negative).
- Removing a *2 factor to the ellipsoid's last parameter (parameter[9] initialisation from compressed matrix).- Changing the test condition for the ellipsoidMatrix eigenvalues (if one of the eigvalues is negative).
- Removing a *2 factor to the ellipsoid's last parameter (parameter[9] initialisation from compressed matrix).Cyril PouponCyril Pouponhttps://framagit.org/cpoupon/gkg/-/merge_requests/17Kokkos remove overlapp modifications2022-04-13T07:21:23ZBrulléKokkos remove overlapp modificationshttps://framagit.org/cpoupon/gkg/-/merge_requests/16Taking glial cell process into consideration in global volume2023-03-20T14:09:08ZBrulléTaking glial cell process into consideration in global volumeCyril PouponCyril Pouponhttps://framagit.org/cpoupon/gkg/-/merge_requests/15Node data distribution2022-04-25T17:20:45ZSimon LegeayNode data distributionCyril PouponCyril Pouponhttps://framagit.org/cpoupon/gkg/-/merge_requests/14Replace GliaPopulation.cxx2022-04-13T07:07:33ZBrulléReplace GliaPopulation.cxx[Glial_Bad_Init](/uploads/3e0b3c7ca6fa342b923490e18166764a/Glial_Bad_Init)
[Glial_Good_Init](/uploads/0e5db582e569030e50f3db9c3bda5521/Glial_Good_Init)
Adding one line on the glial population file to initiate a different center for di...[Glial_Bad_Init](/uploads/3e0b3c7ca6fa342b923490e18166764a/Glial_Bad_Init)
[Glial_Good_Init](/uploads/0e5db582e569030e50f3db9c3bda5521/Glial_Good_Init)
Adding one line on the glial population file to initiate a different center for different glials populations.https://framagit.org/cpoupon/gkg/-/merge_requests/13Mpi test2022-04-25T14:55:08ZSimon LegeayMpi testCyril PouponCyril Pouponhttps://framagit.org/cpoupon/gkg/-/merge_requests/12Json template for simulation2022-04-15T07:51:42ZBrulléJson template for simulationProviding a set of different JSON for launching simulations ( 1 Fiber population, 2 Fiber populations, 3 Fiber populations, 1 Fiber + 1 Astro populations and 2 Fiber + 1 Astro + 1 Oligo populations ).
The JSON files are completed by the ...Providing a set of different JSON for launching simulations ( 1 Fiber population, 2 Fiber populations, 3 Fiber populations, 1 Fiber + 1 Astro populations and 2 Fiber + 1 Astro + 1 Oligo populations ).
The JSON files are completed by the result of a simulation ( .raw file ) the meta data ( .minf ) and the terminal output during the process.
After trying the different populations simulations few issues must be remembered :
- Astrocytes ans oligodendrocytes somas are distributed with the same coordinates ( it must be link to an error of ramdom seed reset)
- Does the process of the glials cell count in the population fraction volume ?
- The beading doesnt work
- The myelin sheath works weirdly, it make appears huge somas at the top and bottom of the fibers ( maybe a simple Json calibration issue ).
All these issues might be fixed trough a future incoming merge request.