VIP: Volume Image Processing
Macros | Functions
brain.h File Reference
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <stdarg.h>
#include <limits.h>
#include <errno.h>
#include <math.h>
#include <vip/util.h>
#include <vip/volume.h>
#include <vip/histo.h>
#include <vip/morpho.h>
#include <vip/talairach.h>
Include dependency graph for brain.h:

Go to the source code of this file.

Macros

#define VOID_LABEL   10
 
#define GRAY_LABEL   100
 
#define BRAIN_LABEL   150
 
#define WHITE_LABEL   200
 
#define FAT_LABEL   220
 

Functions

int VipDilateInPartialVolume (Volume *vol, Volume *mask)
 
int VipDilateInPartialVolumeFar (Volume *vol, Volume *mask, int layer)
 
int VipCreateHistogram (Volume *vol, Volume *mask, Volume *edges, int connectivity)
 
int VipDilateVolumeBorder (Volume *vol, Volume *mask, int T_GRAY_CSF, int T_WHITE_FAT, int connectivity)
 
int VipVolumeEdges (Volume *edges, Vip_S16BIT *edges_ptr, int seuil)
 
int VipCreateBrainSeed (Volume *vol, Volume *var, VipT1HistoAnalysis *ana, int T_GRAY_WHITE, int T_WHITE_FAT, int SEUIL_VAR)
 
int VipPropagationConnectivity (Volume *mask, Volume *vol1, Volume *vol2, int mode, int seuil_vol1, int seuil_vol2, int connectivity)
 
int VipPropagationWithRefluxConnectivity (Volume *mask, Volume *vol, Volume *variance, int distance, int mode, int seuil1, int seuil2, int connectivity)
 
int VipPropagationReflux (Volume *mask, Volume *vol1, Volume *vol2, int nb_iterations, int mode, int seuil_vol1, int seuil_vol2, int connectivity)
 
int VipGetBrain2010 (Volume *vol, Volume *variance, Volume *edges, Volume *ridge, VipT1HistoAnalysis *ana, int dumb, int debug, float brain_erosion_size, int variance_threshold, int nb_iterations, float CA[3], float CP[3], float P[3])
 
int VipGetBrain2005 (Volume *vol, VipT1HistoAnalysis *ana, int dumb, int debug, float opening_size, float max_cortical_thickness, float white_erosion_size, float white_recovering_size, int nb_iterations, Volume *ridge)
 
int VipPutOneSliceTwoZero (Volume *vol, int z)
 
int VipGetBrain (Volume *vol, VipT1HistoAnalysis *ana, int dumb, int debug)
 
int VipGetBrainStandard (Volume *vol, VipT1HistoAnalysis *ana, int dumb, int debug, float brain_erosion_size, float brain_recovering_size, int nb_iterations, int iterative_erosion)
 
int VipGetBrainCustomized (Volume *vol, VipT1HistoAnalysis *ana, int dumb, int debug, float brain_erosion_size, float brain_recovering_size, float white_erosion_size, float white_recovering_size, int nb_iterations, VipTalairach *tal, int iterative_erosion)
 
int VipGetBrainForRenderingDouble (Volume *vol, VipT1HistoAnalysis *ana, int dumb, int debug)
 
int VipFillWhiteCavities (Volume *vol, Volume *brainmask, VipT1HistoAnalysis *ana, int maxsize)
 
int VipGetBrainForRenderingFast (Volume *vol, int dumb, int debug, int Tlow, int Thigh)
 
int VipGetBrainForRenderingFastCustomized (Volume *vol, int dumb, int debug, float brain_erosion_size, float brain_dilation_size, int Tlow, int Thigh)
 
int VipGetBrainForRenderingDoubleCustomized (Volume *vol, VipT1HistoAnalysis *ana, int dumb, int debug, float white_erosion_size, int white_recovering_size, float brain_erosion_size, int brain_recovering_size, int nb_iterations)
 
int VipGetBrainForRenderingSimple (Volume *vol, VipT1HistoAnalysis *ana, int dumb, int debug)
 
int VipGetBrainForRenderingSimpleCustomized (Volume *vol, VipT1HistoAnalysis *ana, int dumb, int debug, float brain_erosion_size, int brain_recovering_size, int nb_iterations)
 
Volume * VipGrayWhiteClassificationRegularisation (Volume *vol, VipT1HistoAnalysis *ana, int dumb)
 
Volume * VipGrayWhiteClassificationRegularisationForVoxelBasedAna (Volume *vol, VipT1HistoAnalysis *ana, int dumb, int nb_iterations, float KPOTTS, int connectivity)
 
Volume * VipGrayWhiteClassificationForVoxelBasedAna (Volume *vol, VipT1HistoAnalysis *ana, float threshold)
 
Volume * VipCSFBrainFatClassificationRegularisation (Volume *vol, VipT1HistoAnalysis *ana, int dumb, int nb_iterations)
 
int VipGrayWhiteClassificationForVoxelBasedNeighbourhood (Volume *vol, Volume *classif, Volume *matter, int dumb, int nb_iterations, int threshold, int connectivity, int label)
 
Volume * VipGrayWhiteRegularisationForVoxelBasedAna (Volume *vol, Volume *classif, VipT1HistoAnalysis *ana, int dumb, int nb_iterations, float KPOTTS, int connectivity)
 
int VipGrayRegularisation (Volume *vol)
 
int VipCleaningTopo (Volume *vol, Volume *matter, Volume *classif, int dumb, int nb_iterations, int label, int threshold)
 
int VipCleaningConnectivity (Volume *vol, int connectivity, int type)
 
Volume * VipCSFGrayWhiteFatClassificationRegularisationForRobustApproach (Volume *vol, VipT1HistoAnalysis *ana, int dumb, int nb_iterations, int T_VOID_GRAY_LOW, int T_VOID_GRAY_HIGH, int T_WHITE_FAT_LOW, int T_WHITE_FAT_HIGH, int T_GRAY_WHITE)
 
Volume * VipCSFGrayWhiteFatClassificationRegularisation (Volume *vol, VipT1HistoAnalysis *ana, int dumb, int nb_iterations)
 
Volume * VipGrayWhiteClassificationRegularisationForRobust (Volume *vol, VipT1HistoAnalysis *ana, int dumb)
 
Volume * VipGrayWhiteClassificationRegularisationForRobust2005 (Volume *vol, VipT1HistoAnalysis *ana, int T_VOID_GRAY_LOW, int T_VOID_GRAY_HIGH, int T_GRAY_WHITE_LOW, int T_GRAY_WHITE_HIGH, int T_WHITE_FAT, int dumb)
 
int VipErosionClassificationNeighbourhood (Volume *classif, Volume *graylevel, VipT1HistoAnalysis *ana, int nb_iteration, int object, int inside, int outside)
 
int VipHomotopicErosionFromInsideSnakeNeighbourhood (Volume *vol, Volume *graylevel, Volume *classif, int nb_iteration, int object, int inside, int outside, float KISING, float sigmaG, float sigmaW, int label)
 
int VipRegularisation (Volume *vol, int label)
 

Macro Definition Documentation

◆ BRAIN_LABEL

#define BRAIN_LABEL   150

Definition at line 48 of file brain.h.

◆ FAT_LABEL

#define FAT_LABEL   220

Definition at line 50 of file brain.h.

◆ GRAY_LABEL

#define GRAY_LABEL   100

Definition at line 47 of file brain.h.

◆ VOID_LABEL

#define VOID_LABEL   10

Definition at line 46 of file brain.h.

◆ WHITE_LABEL

#define WHITE_LABEL   200

Definition at line 49 of file brain.h.

Function Documentation

◆ VipCleaningConnectivity()

int VipCleaningConnectivity ( Volume * vol,
int connectivity,
int type )
extern

◆ VipCleaningTopo()

int VipCleaningTopo ( Volume * vol,
Volume * matter,
Volume * classif,
int dumb,
int nb_iterations,
int label,
int threshold )
extern

◆ VipCreateBrainSeed()

int VipCreateBrainSeed ( Volume * vol,
Volume * var,
VipT1HistoAnalysis * ana,
int T_GRAY_WHITE,
int T_WHITE_FAT,
int SEUIL_VAR )

◆ VipCreateHistogram()

int VipCreateHistogram ( Volume * vol,
Volume * mask,
Volume * edges,
int connectivity )

◆ VipCSFBrainFatClassificationRegularisation()

Volume * VipCSFBrainFatClassificationRegularisation ( Volume * vol,
VipT1HistoAnalysis * ana,
int dumb,
int nb_iterations )
extern

◆ VipCSFGrayWhiteFatClassificationRegularisation()

Volume * VipCSFGrayWhiteFatClassificationRegularisation ( Volume * vol,
VipT1HistoAnalysis * ana,
int dumb,
int nb_iterations )
extern

◆ VipCSFGrayWhiteFatClassificationRegularisationForRobustApproach()

Volume * VipCSFGrayWhiteFatClassificationRegularisationForRobustApproach ( Volume * vol,
VipT1HistoAnalysis * ana,
int dumb,
int nb_iterations,
int T_VOID_GRAY_LOW,
int T_VOID_GRAY_HIGH,
int T_WHITE_FAT_LOW,
int T_WHITE_FAT_HIGH,
int T_GRAY_WHITE )

◆ VipDilateInPartialVolume()

int VipDilateInPartialVolume ( Volume * vol,
Volume * mask )

◆ VipDilateInPartialVolumeFar()

int VipDilateInPartialVolumeFar ( Volume * vol,
Volume * mask,
int layer )

◆ VipDilateVolumeBorder()

int VipDilateVolumeBorder ( Volume * vol,
Volume * mask,
int T_GRAY_CSF,
int T_WHITE_FAT,
int connectivity )

◆ VipErosionClassificationNeighbourhood()

int VipErosionClassificationNeighbourhood ( Volume * classif,
Volume * graylevel,
VipT1HistoAnalysis * ana,
int nb_iteration,
int object,
int inside,
int outside )
extern

◆ VipFillWhiteCavities()

int VipFillWhiteCavities ( Volume * vol,
Volume * brainmask,
VipT1HistoAnalysis * ana,
int maxsize )

◆ VipGetBrain()

int VipGetBrain ( Volume * vol,
VipT1HistoAnalysis * ana,
int dumb,
int debug )

◆ VipGetBrain2005()

int VipGetBrain2005 ( Volume * vol,
VipT1HistoAnalysis * ana,
int dumb,
int debug,
float opening_size,
float max_cortical_thickness,
float white_erosion_size,
float white_recovering_size,
int nb_iterations,
Volume * ridge )

◆ VipGetBrain2010()

int VipGetBrain2010 ( Volume * vol,
Volume * variance,
Volume * edges,
Volume * ridge,
VipT1HistoAnalysis * ana,
int dumb,
int debug,
float brain_erosion_size,
int variance_threshold,
int nb_iterations,
float CA[3],
float CP[3],
float P[3] )

◆ VipGetBrainCustomized()

int VipGetBrainCustomized ( Volume * vol,
VipT1HistoAnalysis * ana,
int dumb,
int debug,
float brain_erosion_size,
float brain_recovering_size,
float white_erosion_size,
float white_recovering_size,
int nb_iterations,
VipTalairach * tal,
int iterative_erosion )

◆ VipGetBrainForRenderingDouble()

int VipGetBrainForRenderingDouble ( Volume * vol,
VipT1HistoAnalysis * ana,
int dumb,
int debug )
extern

◆ VipGetBrainForRenderingDoubleCustomized()

int VipGetBrainForRenderingDoubleCustomized ( Volume * vol,
VipT1HistoAnalysis * ana,
int dumb,
int debug,
float white_erosion_size,
int white_recovering_size,
float brain_erosion_size,
int brain_recovering_size,
int nb_iterations )
extern

◆ VipGetBrainForRenderingFast()

int VipGetBrainForRenderingFast ( Volume * vol,
int dumb,
int debug,
int Tlow,
int Thigh )
extern

◆ VipGetBrainForRenderingFastCustomized()

int VipGetBrainForRenderingFastCustomized ( Volume * vol,
int dumb,
int debug,
float brain_erosion_size,
float brain_dilation_size,
int Tlow,
int Thigh )
extern

◆ VipGetBrainForRenderingSimple()

int VipGetBrainForRenderingSimple ( Volume * vol,
VipT1HistoAnalysis * ana,
int dumb,
int debug )
extern

◆ VipGetBrainForRenderingSimpleCustomized()

int VipGetBrainForRenderingSimpleCustomized ( Volume * vol,
VipT1HistoAnalysis * ana,
int dumb,
int debug,
float brain_erosion_size,
int brain_recovering_size,
int nb_iterations )
extern

◆ VipGetBrainStandard()

int VipGetBrainStandard ( Volume * vol,
VipT1HistoAnalysis * ana,
int dumb,
int debug,
float brain_erosion_size,
float brain_recovering_size,
int nb_iterations,
int iterative_erosion )

◆ VipGrayRegularisation()

int VipGrayRegularisation ( Volume * vol)
extern

◆ VipGrayWhiteClassificationForVoxelBasedAna()

Volume * VipGrayWhiteClassificationForVoxelBasedAna ( Volume * vol,
VipT1HistoAnalysis * ana,
float threshold )
extern

◆ VipGrayWhiteClassificationForVoxelBasedNeighbourhood()

int VipGrayWhiteClassificationForVoxelBasedNeighbourhood ( Volume * vol,
Volume * classif,
Volume * matter,
int dumb,
int nb_iterations,
int threshold,
int connectivity,
int label )
extern

◆ VipGrayWhiteClassificationRegularisation()

Volume * VipGrayWhiteClassificationRegularisation ( Volume * vol,
VipT1HistoAnalysis * ana,
int dumb )
extern

◆ VipGrayWhiteClassificationRegularisationForRobust()

Volume * VipGrayWhiteClassificationRegularisationForRobust ( Volume * vol,
VipT1HistoAnalysis * ana,
int dumb )

◆ VipGrayWhiteClassificationRegularisationForRobust2005()

Volume * VipGrayWhiteClassificationRegularisationForRobust2005 ( Volume * vol,
VipT1HistoAnalysis * ana,
int T_VOID_GRAY_LOW,
int T_VOID_GRAY_HIGH,
int T_GRAY_WHITE_LOW,
int T_GRAY_WHITE_HIGH,
int T_WHITE_FAT,
int dumb )

◆ VipGrayWhiteClassificationRegularisationForVoxelBasedAna()

Volume * VipGrayWhiteClassificationRegularisationForVoxelBasedAna ( Volume * vol,
VipT1HistoAnalysis * ana,
int dumb,
int nb_iterations,
float KPOTTS,
int connectivity )
extern

◆ VipGrayWhiteRegularisationForVoxelBasedAna()

Volume * VipGrayWhiteRegularisationForVoxelBasedAna ( Volume * vol,
Volume * classif,
VipT1HistoAnalysis * ana,
int dumb,
int nb_iterations,
float KPOTTS,
int connectivity )
extern

◆ VipHomotopicErosionFromInsideSnakeNeighbourhood()

int VipHomotopicErosionFromInsideSnakeNeighbourhood ( Volume * vol,
Volume * graylevel,
Volume * classif,
int nb_iteration,
int object,
int inside,
int outside,
float KISING,
float sigmaG,
float sigmaW,
int label )
extern

◆ VipPropagationConnectivity()

int VipPropagationConnectivity ( Volume * mask,
Volume * vol1,
Volume * vol2,
int mode,
int seuil_vol1,
int seuil_vol2,
int connectivity )

◆ VipPropagationReflux()

int VipPropagationReflux ( Volume * mask,
Volume * vol1,
Volume * vol2,
int nb_iterations,
int mode,
int seuil_vol1,
int seuil_vol2,
int connectivity )

◆ VipPropagationWithRefluxConnectivity()

int VipPropagationWithRefluxConnectivity ( Volume * mask,
Volume * vol,
Volume * variance,
int distance,
int mode,
int seuil1,
int seuil2,
int connectivity )

◆ VipPutOneSliceTwoZero()

int VipPutOneSliceTwoZero ( Volume * vol,
int z )
extern

◆ VipRegularisation()

int VipRegularisation ( Volume * vol,
int label )
extern

◆ VipVolumeEdges()

int VipVolumeEdges ( Volume * edges,
Vip_S16BIT * edges_ptr,
int seuil )