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CHANGES.txt
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CHANGES.txt
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------------------------------------------------------------------------
r497 | gaser | 2023-12-06 11:19:15
Changed paths:
M CHANGES.txt
M Progs/CAT_Test.c
M Progs/CAT_VolSanlm.c
Updated CAT_Test.c
------------------------------------------------------------------------
r496 | gaser | 2023-12-06 11:17:52
Changed paths:
M CHANGES.txt
M Lib/CAT_Amap.c
M Progs/CAT_VolAmap.c
Changed defaults and method for bias correction in CAT_VolAmap.c
------------------------------------------------------------------------
r495 | gaser | 2023-12-06 11:17:41
Changed paths:
M CHANGES.txt
M Progs/CAT_VolThicknessPbt.c
Changed: Added option to CAT_VolThicknessPbt.c to skip use of two thickness
measures from sulci and gyri and estimate minimum, but use the simpler
approach based on sulci only.
Changed: Added option to CAT_VolThicknessPbt.c define number of averages
for estimating WM and CSF distance by shifting the border between
GM/WM and GM/CSF to obtain a less noisy measure.
------------------------------------------------------------------------
r470 | gaser | 2023-09-19 23:18:05
Changed paths:
M CHANGES.txt
M Lib/CAT_Amap.c
M Progs/CAT_VolAmap.c
M Progs/CAT_VolAverage.c
M Progs/CAT_VolSmooth.c
Changed: Set ICM iterations to 0 if mrf is also zero in CAT_Amap.c.
Changed: Changed tissue names to BIDS-conforming names in CAT_VolAmap.c.
Changed: reformatted CAT_VolSmooth.c and CAT_VolAverage.c.
------------------------------------------------------------------------
r469 | gaser | 2023-09-13 02:25:36
Changed paths:
M CHANGES.txt
M INSTALL
AM Include/CAT_Amap.h
M Include/CAT_NiftiIO.h
RM Include/niilib.h -> Include/CAT_NiftiLib.h
AM Lib/CAT_Amap.c
M Lib/CAT_NiftiIO.c
RM Lib/niilib.c -> Lib/CAT_NiftiLib.c
M Makefile.am
AM Progs/CAT_VolAmap.c
AM Progs/CAT_VolAverage.c
AM Progs/CAT_VolSmooth.c
M Progs/Makefile.am
M nifti/nifti1_local.h
Changed: Added some tools from amap repository:
CAT_VolAmap
CAT_VolAverage
CAT_VolSmooth
Changed: Added necessary libraries and headers to the new tools.
Changed: Renames niilib.c to CAT_NiftiLib
------------------------------------------------------------------------
r468 | gaser | 2023-09-07 00:24:33
Changed paths:
M CHANGES.txt
Fixed: Skip use of cached volume in CAT_NiftiIO.c
Fixed: Removed initialization of variables in for loop in CAT_Vol.c.
------------------------------------------------------------------------
r467 | gaser | 2023-09-07 00:23:20
Changed paths:
M CHANGES.txt
Fixed: Skip use of cached volume in CAT_NiftiIO.c
Fixed: Removed initialization of variables in for loop in CAT_Vol.c.
------------------------------------------------------------------------
r466 | gaser | 2023-09-07 00:22:58
Changed paths:
M CHANGES.txt
Fixed: Skip use of cached volume in CAT_NiftiIO.c
Fixed: Removed initialization of variables in for loop in CAT_Vol.c.
------------------------------------------------------------------------
r465 | gaser | 2023-09-07 00:11:31
Changed paths:
M CHANGES.txt
M Lib/CAT_NiftiIO.c
M Lib/CAT_Vol.c
M MarchingCubes/MarchingCubes.c
Fixed: Skip use of cached volume in CAT_NiftiIO.c
Fixed: Removed initialization of variables in for loop in CAT_Vol.c.
------------------------------------------------------------------------
r462 | gaser | 2023-04-17 23:12:30
Changed paths:
M CHANGES.txt
A Include/niilib.h
A Lib/niilib.c
Added: Created new niilib.c and niilib.h for additional nifti functions.
------------------------------------------------------------------------
r461 | gaser | 2023-04-17 23:04:09
Changed paths:
M CHANGES.txt
M Include/CAT_NiftiIO.h
M Include/CAT_SurfaceIO.h
M Makefile.am
D Matlab/cg_F2x_curv_txt.m
D Matlab/cg_cov_curv_txt.m
D Matlab/cg_get_aparc_data.m
D Matlab/cg_glm_curv_txt.m
D Matlab/cg_icc_curv_txt.m
D Matlab/cg_invert_values_curv_txt.m
D Matlab/cg_mgh2abs.m
D Matlab/cg_read_curv_txt.m
D Matlab/cg_t2x_curv_txt.m
D Matlab/cg_write_curv_txt.m
D Matlab/create_mean_image_of_each_twinpair_cg.m
D Matlab/load_mgh.m
D Matlab/read_curv.m
D Matlab/save_mgh.m
D Matlab/write_curv.m
M Progs/CAT_DeformMesh.c
M Progs/CAT_MarchingCubesGenus0.c
R not_used_anymore/CAT_FixSelfIntersect.c -> deprecated/CAT_FixSelfIntersect.c
R not_used_anymore/CAT_LBConformalMap.c -> deprecated/CAT_LBConformalMap.c
R not_used_anymore/CAT_LaplaceBeltrami.c -> deprecated/CAT_LaplaceBeltrami.c
R not_used_anymore/CAT_MarchingCubesSphere.c -> deprecated/CAT_MarchingCubesSphere.c
R not_used_anymore/CAT_SelfIntersect.c -> deprecated/CAT_SelfIntersect.c
R not_used_anymore/conjugate.h -> deprecated/conjugate.h
R not_used_anymore/fit_3d.h -> deprecated/fit_3d.h
R not_used_anymore/fit_3d_prototypes.h -> deprecated/fit_3d_prototypes.h
R not_used_anymore/nl/nl.h -> deprecated/nl/nl.h
R not_used_anymore/nl/nl_api.c -> deprecated/nl/nl_api.c
R not_used_anymore/nl/nl_blas.c -> deprecated/nl/nl_blas.c
R not_used_anymore/nl/nl_blas.h -> deprecated/nl/nl_blas.h
R not_used_anymore/nl/nl_context.c -> deprecated/nl/nl_context.c
R not_used_anymore/nl/nl_context.h -> deprecated/nl/nl_context.h
R not_used_anymore/nl/nl_iterative_solvers.c -> deprecated/nl/nl_iterative_solvers.c
R not_used_anymore/nl/nl_iterative_solvers.h -> deprecated/nl/nl_iterative_solvers.h
R not_used_anymore/nl/nl_matrix.c -> deprecated/nl/nl_matrix.c
R not_used_anymore/nl/nl_matrix.h -> deprecated/nl/nl_matrix.h
R not_used_anymore/nl/nl_os.c -> deprecated/nl/nl_os.c
R not_used_anymore/nl/nl_preconditioners.c -> deprecated/nl/nl_preconditioners.c
R not_used_anymore/nl/nl_preconditioners.h -> deprecated/nl/nl_preconditioners.h
R not_used_anymore/nl/nl_private.h -> deprecated/nl/nl_private.h
R not_used_anymore/nl/nl_superlu.c -> deprecated/nl/nl_superlu.c
R not_used_anymore/nl/nl_superlu.h -> deprecated/nl/nl_superlu.h
M gifticlib/gifti_io.h
R niftilib/analyze75.h -> nifti/analyze75.h
R niftilib/nifti1.h -> nifti/nifti1.h
R niftilib/nifti1_io.c -> nifti/nifti1_io.c
RM niftilib/nifti1_io.h -> nifti/nifti1_io.h
RM niftilib/nifti1_local.h -> nifti/nifti1_local.h
R niftilib/znzlib.c -> nifti/znzlib.c
R niftilib/znzlib.h -> nifti/znzlib.h
Changed: Added automatical estimation of dist parameter to
CAT_MarchingCubesGenus0.c.
Changed: Updated help text for CAT_MarchingCubesGenus0.c and changed some
options.
Changed: Renamed folder not_used_anymore to deprecated.
Changed: Renamed folder niftilib to nifti.
Deleted: Deleted Matlab folder that is not necessary anymore.
Added: Created new niilib.c and niilib.h for additional nifti functions.
------------------------------------------------------------------------
r458 | gaser | 2023-03-14 16:17:25
Changed paths:
M .gitignore
M CHANGES.txt
M INSTALL
M Lib/CAT_Vol.c
A Progs/CAT_DeformMesh.c
M Progs/CAT_DeformSurf.c
Changed: Added flag for correcting mesh to cat_DeformSurf.c that allows to
correct mesh w.r.t. local folding to better fit to isovalue.
Fixed: Replaced HUGE by 1e15 in CAT_Vol.c
Added: New CAT_SmoothSharpness.ca nd CAT_DeformMesh.c.
------------------------------------------------------------------------
r457 | gaser | 2023-03-14 07:41:33
Changed paths:
M CHANGES.txt
M Include/CAT_SPH.h
AM Include/CAT_Vol.h
M Lib/CAT_Intersect.c
M Lib/CAT_SPH.c
AM Lib/CAT_Vol.c
M Makefile.am
M Progs/CAT_MarchingCubesGenus0.c
M Progs/Makefile.am
Added: Added CAT_Vaol.c with vollib functions from amap.
Added: Added very preliminary CAT_DeformMesh.c.
Added: Added CAT_SmoothSharpness that weights diffusion smoothing w.r.t.
local sharpness values.
Changes: Removed vollib functions from CAT_MarchingCubesGenus0 and added new
dist-flag that controls amount of morphological openings.
------------------------------------------------------------------------
r456 | gaser | 2023-03-09 23:21:39
Changed paths:
M CHANGES.txt
M Include/CAT_Smooth.h
M Include/CAT_Surf.h
M Lib/CAT_Intersect.c
M Lib/CAT_Smooth.c
M Lib/CAT_Surf.c
M Progs/CAT_3dVol2Surf.c
M Progs/CAT_Central2Pial.c
M Progs/CAT_DumpCurv.c
M Progs/CAT_MarchingCubesGenus0.c
A Progs/CAT_SmoothDiffusion.c
M Progs/CAT_SurfDistance.c
M Progs/Makefile.am
Added: Added new smoothing tool CAT_SmoothDiffusion.c which offers similar
functionality such as CAT_BlurSurfHK.c but by using flags for the many
options.
Changes: Added function to correct meshes in folded areas to compensate for the
averaging effect in gyri and sulci.
Changes: Use the new mesh correction in CAT_SmoothDiffusion.c and
CAT_MarchingCubesGenus0.c.
Changes: Moved some definitions for smoothing to header file.
Changes: Some edits in help text.
------------------------------------------------------------------------
r455 | gaser | 2023-02-12 16:48:46
Changed paths:
M .gitignore
M CHANGES.txt
M Lib/CAT_Refine.c
M Lib/CAT_Smooth.c
M Lib/CAT_Surf.c
M Progs/CAT_Central2Pial.c
M Progs/CAT_SurfDistance.c
M configure.ac
Changes: Added new option for checking self intersections to CAT_Central2Pial.c
that allow to limit correction only after final step, which is much
faster.
Changes: Added option for correction of self intersections
Changes: Changed weighting of averaging in CAT_Smooth.c zo correct number of 3
neighbours.
------------------------------------------------------------------------
r446 | gaser | 2021-10-13 19:13:23
Changed paths:
M CHANGES.txt
M INSTALL
M Progs/CAT_3dVol2Surf.c
M depcomp
M mkinstalldirs
(1) Changed: Updated help text in CAT_3dVol2Surf.c.
------------------------------------------------------------------------
r445 | gaser | 2021-10-13 16:47:49 +0200 (Mi, 13 Okt 2021) | 13 lines
Changed paths:
M CHANGES.txt
M INSTALL
M Lib/CAT_SurfaceIO.c
M Progs/CAT_3dVol2Surf.c
M Progs/CAT_Test.c
M depcomp
(1) Changed: Added new option for writing annot files to CAT_3dVol2Surf.c.
(2) Changed: Added new range option that allows to create masks inside a defined
range to CAT_3dVol2Surf.c.
(3) Changed: Reformatting CAT_SurfaceIO.c.
------------------------------------------------------------------------
r444 | gaser | 2021-08-23 16:46:31 +0200 (Mo, 23 Aug 2021) | 9 lines
Changed paths:
M CHANGES.txt
M Lib/CAT_SurfaceIO.c
M Progs/CAT_BlurSurfHK.c
M configure.ac
(1) Changed: Extended gifti_get_DA_value_2D to also read 64bit float data.
(2) Fixed: Corrected bug in input_gifti_curv to read gifti cdata.
------------------------------------------------------------------------
r443 | gaser | 2021-06-07 12:58:06 +0200 (Mo, 07 Jun 2021) | 8 lines
Changed paths:
M CHANGES.txt
M Lib/CAT_SurfaceIO.c
M Progs/CAT_3dVol2Surf.c
(1) Changed: Updated use of annotation tables in CAT_3dVol2Surf.c.
(2) Fixed: Corrected return argument in read_annotation_table.
------------------------------------------------------------------------
r442 | gaser | 2021-06-03 01:39:50 +0200 (Do, 03 Jun 2021) | 9 lines
Changed paths:
M CHANGES.txt
M Progs/CAT_3dVol2Surf.c
M Progs/CAT_WarpSurfDemon.c
! stamp-h1
(1) Changed: Added median mapping function to CAT_3dVol2Surf.c.
(2) Changed: Updated memory management of median function in CAT_WarpSurfDemon.c.
------------------------------------------------------------------------
r441 | gaser | 2020-11-23 10:21:18 +0100 (Mo, 23 Nov 2020) | 8 lines
Changed paths:
M CHANGES.txt
M Lib/CAT_SurfaceIO.c
Fixed: Replcaed input_texture_values MNI function with own function for reading
txt-files, because of issues with opening files under Windows systems.
------------------------------------------------------------------------
r440 | gaser | 2020-11-13 17:53:59 +0100 (Fr, 13 Nov 2020) | 28 lines
Changed paths:
M CHANGES.txt
M Lib/CAT_Resample.c
M Lib/CAT_SurfaceIO.c
M Progs/CAT_ResampleSphericalSurf.c
M Progs/CAT_ResampleSurf.c
M Progs/CAT_Test.c
M Progs/CAT_WarpSurf.c
M Progs/CAT_WarpSurfDemon.c
M dartel/dartel.h
M dartel/diffeosphere.c
M dartel/optimizersphere.c
! stamp-h1
(1) Changed: Adapted optimizersphere.c to newer changes in optimizer2d.c.
(2) Changed: Added preliminary support for weighting output deformations w.r.t.
distance to pole regions (not yileding better results).
(3) Changed: Updated multi-step support for CAT_WarpDemon.c
(4) Fixed: Corrected output and handling for label interpolation.
(5) Fixed: Disapled resampling of annotazion files which is not yet working
for Windows systems.
(6) Fixed: Corrected allocation in CAT_ResampleSphericalSurf.c which was in
wrong order.
(7) Fixed: Corrected output of txt-files for double and integer format, which
is now using starighforward fprintf function.
(8) Fixed: ULONG_MAX was not correctly defined and caused wrong estimation of
minimum values in resample_surface_to_target_sphere function.
------------------------------------------------------------------------
r439 | gaser | 2020-09-24 17:47:46 +0200 (Do, 24 Sep 2020) | 9 lines
Changed paths:
M CHANGES.txt
M INSTALL
M Progs/CAT_3dVol2Surf.c
M mkinstalldirs
Changed: Added preliminary handling of annotation files to CAT_3dVol2Surf.c
which does not work yet.
------------------------------------------------------------------------
r438 | gaser | 2020-09-17 12:08:10 +0200 (Do, 17 Sep 2020) | 9 lines
Changed paths:
M CHANGES.txt
M INSTALL
M MarchingCubes/genus0.c
! depcomp
M mkinstalldirs
(1) Changed: Updated MarchingCubes/genus0.c with the newest changes from CAT12.
------------------------------------------------------------------------
r437 | gaser | 2020-05-15 13:11:22 +0200 (Fr, 15 Mai 2020) | 9 lines
Changed paths:
M CHANGES.txt
M Include/CAT_Resample.h
M Lib/CAT_Resample.c
! stamp-h1
(1) Fixed: Changed data type in CAT_ResampleSurf.c to prevent overflow.
(2) Changed: Updated header information for CAT_ResampleSurf.?
------------------------------------------------------------------------
r436 | gaser | 2020-05-15 12:50:37 +0200 (Fr, 15 Mai 2020) | 8 lines
Changed paths:
M CHANGES.txt
M Lib/CAT_Resample.c
Changed: Updated label interpolation in CAT_Resample to increase speed for
very large and sparse label entries.
------------------------------------------------------------------------
r435 | gaser | 2020-02-24 11:46:23 +0100 (Mo, 24 Feb 2020) | 12 lines
Changed paths:
M CHANGES.txt
M Include/CAT_Surf.h
M Lib/CAT_Surf.c
M Progs/CAT_DumpSurfaceRatio.c
! stamp-h1
(1) Changed: Added option to switch off normalization for surface ratio
estimation.
(2) Changed: Added normalization for automatically estimated radius for surface
ratio.
------------------------------------------------------------------------
r434 | gaser | 2020-02-13 10:54:29 +0100 (Do, 13 Feb 2020) | 10 lines
Changed paths:
M CHANGES.txt
M Progs/CAT_3dVol2Surf.c
M dartel/diffeosphere.c
M dartel/optimizersphere.c
! stamp-h1
(1) Changed: Added some OpenMP-code snippets to 2D dartel registration.
(2) Fixed: Direction of equivolume mapping for CAT_3dVol2Surf.c was inverted.
------------------------------------------------------------------------
r433 | gaser | 2020-01-16 22:40:29 +0100 (Do, 16 Jan 2020) | 8 lines
Changed paths:
M CHANGES.txt
M Lib/CAT_Defect.c
MM not_used_anymore/CAT_MarchingCubesSphere.c
M not_used_anymore/conjugate.h
Changed: Corrected use of delete_object_list.
------------------------------------------------------------------------
r432 | gaser | 2020-01-16 22:29:02 +0100 (Do, 16 Jan 2020) | 9 lines
Changed paths:
A + CHANGES.txt
M Lib/CAT_Complexity.c
M Lib/CAT_Defect.c
(1) Fixed: Corrected bug in CAT_Complexity.c where an object was removed
incorrectly that cause a crash.
(2) Changed: Added change from last revision in CAT_Defects.c again.
------------------------------------------------------------------------
r431 | gaser | 2020-01-14 08:34:27 +0100 (Di, 14 Jan 2020) | 12 lines
Changed paths:
M Lib/CAT_Complexity.c
M Lib/CAT_Curvature.c
M Lib/CAT_Defect.c
M Lib/CAT_Gyrification.c
M Lib/CAT_SPH.c
M Progs/CAT_DumpGyrificationIndex.c
M Progs/CAT_FractalDimension.c
! stamp-h1
Changed: Added or replaced delete_object_list call where needed.
------------------------------------------------------------------------
r430 | gaser | 2020-01-13 18:30:01 +0100 (Mo, 13 Jan 2020) | 50 lines
Changed paths:
D CHANGES.txt
M INSTALL
D Include/conjugate.h
D Include/fit_3d.h
> moved to not_used_anymore/fit_3d.h
D Include/fit_3d_prototypes.h
> moved to not_used_anymore/fit_3d_prototypes.h
M Lib/CAT_Curvature.c
M Lib/CAT_Defect.c
D Lib/CAT_LaplaceBeltrami.c
> moved to not_used_anymore/CAT_LaplaceBeltrami.c
M Lib/CAT_SPH.c
D Lib/CAT_SelfIntersect.c
> moved to not_used_anymore/CAT_SelfIntersect.c
M Lib/CAT_Topology.c
M Makefile.am
D Progs/CAT_FixSelfIntersect.c
> moved to not_used_anymore/CAT_FixSelfIntersect.c
D Progs/CAT_LBConformalMap.c
> moved to not_used_anymore/CAT_LBConformalMap.c
M Progs/Makefile.am
M depcomp
M mkinstalldirs
D nl
> moved to not_used_anymore/nl
A not_used_anymore
A + not_used_anymore/CAT_FixSelfIntersect.c
> moved from Progs/CAT_FixSelfIntersect.c
A + not_used_anymore/CAT_LBConformalMap.c
> moved from Progs/CAT_LBConformalMap.c
A + not_used_anymore/CAT_LaplaceBeltrami.c
> moved from Lib/CAT_LaplaceBeltrami.c
A not_used_anymore/CAT_MarchingCubesSphere.c
A + not_used_anymore/CAT_SelfIntersect.c
> moved from Lib/CAT_SelfIntersect.c
A not_used_anymore/conjugate.h
A + not_used_anymore/fit_3d.h
> moved from Include/fit_3d.h
A + not_used_anymore/fit_3d_prototypes.h
> moved from Include/fit_3d_prototypes.h
A + not_used_anymore/nl
> moved from nl
(1) Fixed: Weird error in CAT_FixTopology-code that caused inconsistency of
resulting fixed surfaces.
(2) Removed: Deleted Laplace-Beltrami Conformal mapping that was not used
anymore.
(3) Removed: Also removed NL-library and tested Selfintersction code.
------------------------------------------------------------------------
r429 | gaser | 2019-12-18 01:12:23 +0100 (Mi, 18 Dez 2019) | 11 lines
Changed paths:
M CHANGES.txt
M Lib/CAT_SelfIntersect.c
M Makefile.am
M Progs/CAT_FixSelfIntersect.c
(1) Changed: Updated CAT_FixSelfIntersect.c to iteratively minimize self-
intersections.
(2) Chnaged: Added subfunction for fixing self-intersections to
CAT_SelfIntersect.c
------------------------------------------------------------------------
r428 | gaser | 2019-12-17 22:18:26 +0100 (Di, 17 Dez 2019) | 11 lines
Changed paths:
A CHANGES.txt
M INSTALL
A Include/conjugate.h
M Progs/Makefile.am
M depcomp
M mkinstalldirs
Added: CHANGES.txt
------------------------------------------------------------------------
r427 | gaser | 2019-10-23 10:19:42 +0200 (Mi, 23 Okt 2019) | 6 lines
Changed paths:
M Progs/CAT_SurfDistance.c
! stamp-h1
Fixed: Corrected handling with input arguments in CAT_SurfDistance.c
------------------------------------------------------------------------
r426 | gaser | 2019-10-16 12:13:52 +0200 (Mi, 16 Okt 2019) | 10 lines
Changed paths:
M Include/fit_3d.h
M Include/fit_3d_prototypes.h
M Lib/CAT_SelfIntersect.c
MM Progs/CAT_FixSelfIntersect.c
M Progs/CAT_SurfDistance.c
! stamp-h1
Fixed: Corrected handling with input arguments in CAT_SurfDistance.c
------------------------------------------------------------------------
r425 | gaser | 2019-09-30 16:39:39 +0200 (Mo, 30 Sep 2019) | 6 lines
Changed paths:
M Progs/CAT_ResampleFS_ui
M Progs/CAT_ResampleSurf.c
Fixed: CAT_ResampleSurf.c now also accepts NULL inputs for selected parameters.
------------------------------------------------------------------------
r424 | gaser | 2019-09-30 00:27:52 +0200 (Mo, 30 Sep 2019) | 11 lines
Changed paths:
M Include/CAT_Map.h
M Lib/CAT_Resample.c
M Makefile.am
M Progs/CAT_ResampleSurf.c
M Progs/Makefile.am
(1) Changed: Removed some unneccessary functions in CAT_Map.c.
(2) Changed: Added label interpolation to CAT_Resample.c
------------------------------------------------------------------------
r423 | gaser | 2019-09-13 11:51:36 +0200 (Fr, 13 Sep 2019) | 11 lines
Changed paths:
A Include/fit_3d.h
A Include/fit_3d_prototypes.h
A Lib/CAT_SelfIntersect.c
M Makefile.am
A Progs/CAT_FixSelfIntersect.c
M Progs/Makefile.am
Changed: Added new code from civet surface_extraction for fixing
selfintersections.
------------------------------------------------------------------------
r422 | gaser | 2019-09-02 09:49:15 +0200 (Mo, 02 Sep 2019) | 12 lines
Changed paths:
M Lib/CAT_DeformPolygons.c
M Progs/CAT_DeformSurf.c
! stamp-h1
(1) Changed: Check for intersections in CAT_DeformSurf is changed to every 100
iterations.
(2) Changed: Print message if stopping criteria was reached in
CAT_DeformPolygons.c to potentially catch that. Furthermore, the check for
intersectiuons is now additionally applied at the beginning and some
unnecessary code was removed.
------------------------------------------------------------------------
r421 | gaser | 2019-08-26 17:28:45 +0200 (Mo, 26 Aug 2019) | 8 lines
Changed paths:
M Lib/CAT_Map.c
D Progs/CAT_Obj2Neurolens
MM Progs/CAT_SurfDistance.c
(1) Changed: Cleaned code in CAT_Maps.c.
(2) Changed: Removed CAT_Obj2Neurolens.
------------------------------------------------------------------------
r420 | gaser | 2019-08-15 00:30:02 +0200 (Do, 15 Aug 2019) | 7 lines
Changed paths:
M Lib/CAT_Intersect.c
Changed: Added stopping criteria for correction of self-intersections
in CAT_Intersect.c.
------------------------------------------------------------------------
r419 | gaser | 2019-08-14 15:02:13 +0200 (Mi, 14 Aug 2019) | 9 lines
Changed paths:
M Lib/CAT_Surf.c
M Progs/CAT_DeformSurf.c
M Progs/CAT_SurfDistance.c
(1) Changed: Removed debugging code.
(2) Changed: Lowered number of check_every_iteration to 20 in
CAT_DeformSurf.c.
------------------------------------------------------------------------
r418 | gaser | 2019-08-14 00:10:40 +0200 (Mi, 14 Aug 2019) | 12 lines
Changed paths:
M Include/CAT_Surf.h
M Lib/CAT_Surf.c
M Progs/CAT_Hausdorff.c
A Progs/CAT_SurfDistance.c
M Progs/Makefile.am
(1) Changed: Added function to calculate distances between two surfaces.
Instead of defining two surfaces you can also use the thickness flag
and the central surface to obtain inner and outer surface.
(2) Changed: Added verbose flag to compute_exact_hausdorff in CAT_Surf.c
------------------------------------------------------------------------
r417 | gaser | 2018-08-29 12:49:17 +0200 (Mi, 29 Aug 2018) | 13 lines
Changed paths:
M Lib/CAT_DeformPolygons.c
M Progs/CAT_3dVol2Surf.c
M Progs/CAT_DeformSurf.c
! stamp-h1
(1) Fixed: Error in CAT_3dVol2Surf.c for equivolume option that crashed
sometimes.
(2) Changed: Lowered number of check_every_iteration to 20 in
CAT_DeformSurf.c.
(3) Changed: Lower number of iterations for smoothing selfintersections
in deform_polygons_check_selfintersection.
------------------------------------------------------------------------
r416 | gaser | 2018-08-24 09:29:04 +0200 (Fr, 24 Aug 2018) | 6 lines
Changed paths:
M Progs/CAT_RefineMesh.c
! stamp-h1
Fixed: Typo in CAT_RefineMesh.c
------------------------------------------------------------------------
r415 | gaser | 2018-08-23 21:24:03 +0200 (Do, 23 Aug 2018) | 15 lines
Changed paths:
M Include/CAT_Refine.h
M Lib/CAT_ConvexHull.c
M Lib/CAT_Refine.c
M Lib/CAT_Surf.c
M Lib/CAT_Topology.c
M Progs/CAT_3dVol2Surf.c
M Progs/CAT_RefineMesh.c
(1) Changed: Added curvature weighting to CAT_RefineMesh.c to force better
refining in areas with large absolute mean curvature (e.g. sulci and gyri).
This will utilize better surface deforming in these areas.
(2) Changed: Updated functions that call refine_mesh that covers the new
changes.
------------------------------------------------------------------------
r414 | gaser | 2018-08-17 15:27:20 +0200 (Fr, 17 Aug 2018) | 14 lines
Changed paths:
M Include/CAT_DeformPolygons.h
M Lib/CAT_DeformPolygons.c
M Lib/CAT_Intersect.c
M Lib/CAT_Surf.c
M Lib/CAT_Topology.c
M Progs/CAT_DeformSurf.c
M Progs/CAT_WarpSurf.c
(1) Changed: Added option to force no self intersections to
deform_polygons_check_selfintersection.
(2) Changed: Updated all functions that call
deform_polygons_check_selfintersection.
------------------------------------------------------------------------
r413 | gaser | 2018-05-02 11:32:30 +0200 (Mi, 02 Mai 2018) | 6 lines
Changed paths:
M Include/CAT_Surf.h
M Progs/CAT_SPH2Surf.c
Changed: Added option to correct for bounding box in CAT_SPH2Surf.c
------------------------------------------------------------------------
r412 | gaser | 2018-04-24 10:12:53 +0200 (Di, 24 Apr 2018) | 13 lines
Changed paths:
M Include/CAT_DeformPolygons.h
M Include/CAT_Intersect.h
M Lib/CAT_DeformPolygons.c
M Lib/CAT_Intersect.c
M Lib/CAT_Topology.c
M Progs/CAT_BlurSurfHK.c
M Progs/CAT_DeformSurf.c
M Progs/Makefile.am
! stamp-h1
Changed: Increased number of iterations for checking self intersections.
------------------------------------------------------------------------
r411 | gaser | 2018-04-09 14:29:04 +0200 (Mo, 09 Apr 2018) | 5 lines
Changed paths:
M Progs/CAT_DeformSurf_ui
Fixed: CAT_DeformSurf_ui ignored first step of deformations.
------------------------------------------------------------------------
r410 | gaser | 2018-03-27 21:15:15 +0200 (Di, 27 Mär 2018) | 7 lines
Changed paths:
M Lib/CAT_Surf.c
! stamp-h1
Changed: Updated check for self intersections in CAT_Surf.c that is now using
decreasing step width for each step.
------------------------------------------------------------------------
r409 | gaser | 2018-03-16 14:26:50 +0100 (Fr, 16 Mär 2018) | 11 lines
Changed paths:
M Include/CAT_Surf.h
M Lib/CAT_Surf.c
M Progs/CAT_3dVol2Surf.c
M Progs/CAT_Central2Pial.c
M Progs/CAT_SelfIntersect.c
M Progs/Makefile.am
Changed: Added check for self intersections in CAT_Central2Pial and
subfunctions in CAT_Surf.c
------------------------------------------------------------------------
r408 | gaser | 2018-01-26 15:04:56 +0100 (Fr, 26 Jan 2018) | 8 lines
Changed paths:
M Progs/CAT_3dVol2Surf.c
! stamp-h1
Changed: Changed output names that are now indicated according to
the used approach (ev or ed for equi-volume or equi-distance) in
CAT_3DVol2Surf.c
------------------------------------------------------------------------
r407 | gaser | 2018-01-26 11:59:17 +0100 (Fr, 26 Jan 2018) | 7 lines
Changed paths:
M Progs/CAT_3dVol2Surf.c
M Progs/CAT_ResampleSurf.c
Changed: Added option for mapping data for each grid step separately and save
file with indicated grid value in CAT_3DVol2Surf.c
------------------------------------------------------------------------
r406 | gaser | 2018-01-25 23:51:04 +0100 (Do, 25 Jan 2018) | 11 lines
Changed paths:
M Include/CAT_Surf.h
M Lib/CAT_Surf.c
M Progs/CAT_3dVol2Surf.c
M Progs/CAT_Central2Pial.c
(1) Changed: Outsourcing function for getting surface area of surface that
was shited along normals to CAT_Surf.c.
(2) Changed: Using outsourced function for surface area in CAT_Central2Pial.c
(3) Changed: Added Bok's equivolume model to CAT_3DVol2Surf.c.
------------------------------------------------------------------------
r405 | gaser | 2018-01-23 10:06:48 +0100 (Di, 23 Jan 2018) | 9 lines
Changed paths:
M Include/CAT_Surf.h
M Lib/CAT_Surf.c
M Progs/CAT_Hausdorff.c
M Progs/CAT_MarchingCubes.c
M Progs/CAT_MarchingCubesGenus0.c
Changed: Added closest distance option to CAT_Hausdorff.c
------------------------------------------------------------------------
r404 | gaser | 2018-01-19 16:54:06 +0100 (Fr, 19 Jan 2018) | 8 lines
Changed paths:
M Lib/CAT_Surf.c
M Progs/CAT_Central2Pial.c
M Progs/CAT_SelfIntersect.c
! stamp-h1
Changed: Removed findal smoothing for expension from central to pial surface.
------------------------------------------------------------------------
r403 | gaser | 2018-01-18 15:24:31 +0100 (Do, 18 Jan 2018) | 27 lines
Changed paths:
M Include/CAT_Complexity.h
M Include/CAT_ConvexHull.h
M Include/CAT_Defect.h
M Include/CAT_FixTopology.h
M Include/CAT_Intersect.h
M Include/CAT_Map.h
M Include/CAT_NiftiIO.h
M Include/CAT_Octree.h
M Include/CAT_Refine.h
M Include/CAT_Resample.h
M Include/CAT_SPH.h
M Include/CAT_Separate.h
M Include/CAT_Surf.h
M Lib/CAT_DeformPolygons.c
M Lib/CAT_NiftiIO.c
M Lib/CAT_Surf.c
M Progs/CAT_Central2Pial.c
M Progs/CAT_SulcusDepth.c
M Progs/CAT_WarpSurf.c
(1) Changed: Moved function for getting pial from central surface to CAT_Surf.c
(2) Changed: Added equi-volume model and weighting to CAT_Central2Pial.c
(3) Changed: Some cosmetic changes in header files
(4) Fixed: Removed 4th dimension in input function in CAT_NiftiIO.c that caused
issues on some systems.
------------------------------------------------------------------------
r402 | gaser | 2018-01-08 16:15:59 +0100 (Mo, 08 Jan 2018) | 7 lines
Changed paths:
M Progs/CAT_DumpSurfaceRatio.c
Changed: The surface ratio estimation is now correcting the radius for individual
surface area so that the approach is scaling invariant. As reference total
surface area the template mesh from CAT12 is used with a surface area of 90000mm^2.
------------------------------------------------------------------------
r401 | gaser | 2018-01-08 12:10:11 +0100 (Mo, 08 Jan 2018) | 10 lines
Changed paths:
M Lib/CAT_Surf.c
M Progs/CAT_DumpGyrificationIndex.c
M Progs/CAT_DumpSurfArea.c
M Progs/CAT_DumpSurfaceRatio.c
Changed: The surface ratio estimation is now correcting the radius for individual
surface area so that the approach is scaling invariant. As reference total
surface area the template mesh from CAT12 is used with a surface area of 90000mm^2.
------------------------------------------------------------------------
r400 | gaser | 2018-01-07 23:03:28 +0100 (So, 07 Jan 2018) | 9 lines
Changed paths:
M Lib/CAT_Surf.c
M Progs/CAT_DumpSurfArea.c
M Progs/CAT_DumpSurfaceRatio.c
Changed: Added automatical estimation of optimal radius to surface ratio
approach. This radius will result in a global (mean) surface ratio that
is equal to the global gyrification index.
------------------------------------------------------------------------
r399 | gaser | 2017-12-21 11:37:16 +0100 (Do, 21 Dez 2017) | 7 lines
Changed paths:
M Progs/CAT_3dVol2Surf.c
Changed: Weighted average with gaussian kernel is now using an extended
gaussian kernel that has weighting of 0.5 at the borders but is also
defined outside the borders up to a weight of around 0.1.
------------------------------------------------------------------------
r398 | gaser | 2017-12-19 11:15:09 +0100 (Di, 19 Dez 2017) | 9 lines
Changed paths:
M Lib/CAT_Curvature.c
M Progs/CAT_DumpCurv.c
M Progs/CAT_Surf2Sheet.c
M Progs/CAT_WarpSurf.c
(1) Changed: Surface Smoothing for CAT_WarpSurf is now set to "0" as default.
(2) Changed: Added depth potential to CAT_DumCurv and CAT_WarpSurf.
------------------------------------------------------------------------
r397 | gaser | 2017-12-18 00:04:42 +0100 (Mo, 18 Dez 2017) | 6 lines
Changed paths:
M Lib/CAT_DepthPotential.c
Fixed: CAT_DepthPotential had difficulties with resampled surfaces and
resulted in NaNs.
------------------------------------------------------------------------
r396 | gaser | 2017-12-15 23:16:54 +0100 (Fr, 15 Dez 2017) | 7 lines
Changed paths:
M Lib/CAT_Curvature.c
M Progs/CAT_WarpSurf.c
(1) Changed: Added options for curvtypes for each step in CAT_WarpSurf.c.
(2) Changed: Added option for depth potential in CAT_Curvature.c
------------------------------------------------------------------------
r395 | gaser | 2017-12-15 12:15:46 +0100 (Fr, 15 Dez 2017) | 16 lines
Changed paths:
M Lib/CAT_Complexity.c
M Lib/CAT_Curvature.c
M Lib/CAT_Refine.c
M Lib/CAT_Smooth.c
M Lib/CAT_Surf.c
M Progs/CAT_WarpSurf.c
(1) Fixed: Heat kernel Smoothing was resolution dependent. Solved that issue
and additionally replaced the weighting for filtering meshes with equal
weighting. Sigma is now the mean point distance.
(2) Changed: Changed smoothing parameters to be compatible to the old
smoothing for internal mesh smoothing:
CAT_WarpSurf: fwhm_surf = 20.0
CAT_Curvature: FWHM for sulcal depth like estimator 50.0
------------------------------------------------------------------------
r394 | gaser | 2017-11-30 09:21:39 +0100 (Do, 30 Nov 2017) | 9 lines
Changed paths:
M Lib/CAT_NiftiIO.c
D Progs/CAT_3dVol2Surf_multi.c
M Progs/CAT_WarpSurf.c
! stamp-h1
Changed: Changed back number of steps to 2 by default in CAT_WarpSurf.c
------------------------------------------------------------------------
r393 | gaser | 2017-11-29 16:52:58 +0100 (Mi, 29 Nov 2017) | 9 lines
Changed paths: