static int
compute_rigid_gradient(MRI_SURFACE *mris, MRI *mri, double *pdx, double *pdy, double *pdz) {
int vno ;
VERTEX *v ;
Real val, xw, yw, zw, dx, dy, dz, delV, x, y, z, Ix, Iy, Iz, xv, yv, zv ;
dx = dy = dz = 0.0 ;
for (vno = 0 ; vno < mris->nvertices ; vno++) {
v = &mris->vertices[vno] ;
if (v->ripflag)
continue ;
if (vno == Gdiag_no)
DiagBreak() ;
x = v->x ;
y = v->y ;
z = v->z ;
MRISvertexToVoxel(mris, v, mri, &xw, &yw, &zw);
MRIsampleVolume(mri, xw, yw, zw, &val) ;
MRIsampleVolumeGradient(mri, xw, yw, zw, &Ix, &Iy, &Iz) ;
// convert back to surface coords
xw += Ix ;
yw += Iy ;
zw += Iz ;
if (mris->useRealRAS)
MRIvoxelToWorld(mri, xw, yw, zw, &xv, &yv, &zv) ;
else
MRIvoxelToSurfaceRAS(mri, xw, yw, zw, &xv, &yv, &zv) ;
Ix = xv-v->x ;
Iy = yv-v->y;
Iz = zv-v->z ;
delV = v->val - val ;
dx += delV * Ix ;
dy += delV * Iy ;
dz += delV * Iz ;
if (!finitep((float)dx))
DiagBreak() ;
if (!finitep((float)dy))
DiagBreak() ;
if (!finitep((float)dz))
DiagBreak() ;
}
dx /= mris->nvertices ;
dy /= mris->nvertices ;
dz /= mris->nvertices ;
*pdx = dx ;
*pdy = dy ;
*pdz = dz ;
return(NO_ERROR) ;
}
void LayerFCD::UpdateRASImage( vtkImageData* rasImage)
{
if (!m_fcd)
{
return;
}
int n[3];
double pos[3];
int* dim = rasImage->GetDimensions();
memset( rasImage->GetScalarPointer(),
0,
dim[0] * dim[1] * dim[2] * rasImage->GetScalarSize() );
if ( m_fcd->nlabels == 0 )
{
cout << "No labels found\n";
return;
}
for (int cnt = 0; cnt < m_fcd->nlabels; cnt++)
{
LABEL* label = m_fcd->labels[cnt];
FSVolume* ref_vol = m_layerSource->GetSourceVolume();
for ( int i = 0; i < label->n_points; i++ )
{
pos[0] = label->lv[i].x;
pos[1] = label->lv[i].y;
pos[2] = label->lv[i].z;
if ( label->coords == LABEL_COORDS_VOXEL )
{
MRIvoxelToWorld(ref_vol->GetMRI(),
pos[0], pos[1], pos[2],
pos, pos+1, pos+2);
}
else if (label->coords == LABEL_COORDS_TKREG_RAS)
{
ref_vol->TkRegToNativeRAS( pos, pos );
}
ref_vol->NativeRASToRAS( pos, pos );
ref_vol->RASToTargetIndex( pos, n );
if ( n[0] >= 0 && n[0] < dim[0] && n[1] >= 0 && n[1] < dim[1] &&
n[2] >= 0 && n[2] < dim[2] )
{
rasImage->SetScalarComponentFromFloat
( n[0], n[1], n[2], 0, label->lv[i].vno );
}
}
}
}
void LayerFCD::SetLabelVisible(int nIndex, bool visible)
{
LABEL* label = m_fcd->labels[nIndex];
FSVolume* ref_vol = m_layerSource->GetSourceVolume();
int n[3];
double pos[3];
int* dim = m_imageData->GetDimensions();
for ( int i = 0; i < label->n_points; i++ )
{
pos[0] = label->lv[i].x;
pos[1] = label->lv[i].y;
pos[2] = label->lv[i].z;
if ( label->coords == LABEL_COORDS_VOXEL )
{
MRIvoxelToWorld(ref_vol->GetMRI(),
pos[0], pos[1], pos[2],
pos, pos+1, pos+2);
}
else if (label->coords == LABEL_COORDS_TKREG_RAS)
{
ref_vol->TkRegToNativeRAS( pos, pos );
}
ref_vol->NativeRASToRAS( pos, pos );
ref_vol->RASToTargetIndex( pos, n );
if ( n[0] >= 0 && n[0] < dim[0] && n[1] >= 0 && n[1] < dim[1] &&
n[2] >= 0 && n[2] < dim[2] )
{
m_imageData->SetScalarComponentFromFloat
( n[0], n[1], n[2], 0, visible?label->lv[i].vno:0 );
}
}
for (int i = 0; i < 3; i++)
{
mReslice[i]->Modified();
}
emit ActorUpdated();
}
void LayerFCD::GetLabelCentroidPosition(int nLabelIndex, double *pos)
{
if (nLabelIndex >= m_fcd->nlabels)
{
return;
}
LABEL* label = m_fcd->labels[nLabelIndex];
if (label->n_points > 0)
{
double x = 0, y = 0, z = 0;
for ( int i = 0; i < label->n_points; i++ )
{
x += label->lv[i].x;
y += label->lv[i].y;
z += label->lv[i].z;
}
pos[0] = x / label->n_points;
pos[1] = y / label->n_points;
pos[2] = z / label->n_points;
FSVolume* ref_vol = m_layerSource->GetSourceVolume();
if ( label->coords == LABEL_COORDS_VOXEL )
{
MRIvoxelToWorld(ref_vol->GetMRI(),
pos[0], pos[1], pos[2],
pos, pos+1, pos+2);
}
else if (label->coords == LABEL_COORDS_TKREG_RAS)
{
ref_vol->TkRegToNativeRAS( pos, pos );
}
ref_vol->NativeRASToRAS( pos, pos );
m_layerSource->RASToTarget(pos, pos);
}
}
/*
* check
*
* conduct a sanity check of particular labels, most importantly
* hippocampus, that such labels do not exist in talairach coords
* where they are known not to belong (indicating a bad manual edit)
*/
static int check(MRI *mri_seg, char *subjects_dir, char *subject_name)
{
int x, y, z, label, errors=0;
Real xw=0.0, yw=0.0, zw=0.0; // RAS coords
Real xmt=0.0, ymt=0.0, zmt=0.0; // MNI tal coords
float xt=0.0, yt=0.0, zt=0.0; // 'real' tal coords
MRI *mri_fixed = NULL;
float max_xtal_l_hippo = -1000;
float max_xtal_l_caudate = -1000;
float max_xtal_l_amygdala = -1000;
float max_xtal_l_putamen = -1000;
float max_xtal_l_pallidum = -1000;
float min_xtal_r_hippo = 1000;
float min_xtal_r_caudate = 1000;
float min_xtal_r_amygdala = 1000;
float min_xtal_r_putamen = 1000;
float min_xtal_r_pallidum = 1000;
printf("checking labels in subject %s...\n",subject_name);
if (do_fix_badsubjs)
{
mri_fixed = MRIcopy(mri_seg,NULL);
}
if (NULL == mri_seg->linear_transform)
{
ErrorExit(ERROR_BADFILE,
"ERROR: mri_ca_train: talairach.xfm not found in %s!\n"
"Run mri_add_xform_to_header to add to volume.\n",
seg_dir);
}
// now conduct checks for voxels in locations where they shouldnt be
for (x = 0 ; x < mri_seg->width ; x++)
{
for (y = 0 ; y < mri_seg->height ; y++)
{
for (z = 0 ; z < mri_seg->depth ; z++)
{
/*
* rules:
* - no label should have a voxel coord < 6 or > 249
* - no left or right hippo labels with z tal coord > 15
* - no left hippo, caudate, amydala, putamen or pallidum
* labels with x tal coord > 5 (or right, with x tal coord < -5)
*/
label = MRIgetVoxVal(mri_seg, x, y, z, 0) ;
int proper_label = label; // used for making corrections
if (label != Unknown)
{
// note: these won't be caught if -mask brainmask.mgz is included
// on the command-line, since voxels outside of brainmask get
// labelled as Unknown.
if ((x < 6) || (y < 6) || (z < 6) ||
(x > 249) || (y > 249) || (z > 249))
{
printf
("ERROR: %s: found label outside of brain: "
"%d %d %d\n",
cma_label_to_name(label),x,y,z);
fflush(stdout) ;
errors++;
proper_label = Unknown;
}
}
if ((label == Left_Hippocampus) || (label == Right_Hippocampus) ||
(label == Left_Caudate) || (label == Right_Caudate) ||
(label == Left_Amygdala) || (label == Right_Amygdala) ||
(label == Left_Putamen) || (label == Right_Putamen) ||
(label == Left_Pallidum) || (label == Right_Pallidum) ||
(label == Left_Inf_Lat_Vent) || (label == Right_Inf_Lat_Vent))
{
// the 'if' statement above spares some cpu cycles in having to
// calculate the coord transform for every voxel, ie these 3 lines:
MRIvoxelToWorld(mri_seg, x, y, z, &xw, &yw, &zw) ;
transform_point(mri_seg->linear_transform,
xw, yw, zw, &xmt, &ymt, &zmt);// get mni tal coords
FixMNITal(xmt,ymt,zmt, &xt,&yt,&zt); // get 'real' tal coords
switch (label)
{
case Left_Hippocampus:
if (zt > 15)
{
printf
("ERROR: %s: "
"%d %d %d, tal x=%f, y=%f, *** z=%f > 15 ***\n",
cma_label_to_name(label),x,y,z,xt,yt,zt);
fflush(stdout) ;
errors++;
}
// no break (check xt)
case Left_Caudate:
case Left_Amygdala:
case Left_Putamen:
case Left_Pallidum:
case Left_Inf_Lat_Vent:
if (xt > 5)
{
printf
("ERROR: %s: "
"%d %d %d, tal *** x=%f > 5 ***, y=%f, z=%f\n",
cma_label_to_name(label), x,y,z,xt,yt,zt);
fflush(stdout) ;
errors++;
if (label == Left_Hippocampus) proper_label = Right_Hippocampus;
else if (label == Left_Caudate) proper_label = Right_Caudate;
else if (label == Left_Amygdala) proper_label = Right_Amygdala;
else if (label == Left_Putamen) proper_label = Right_Putamen;
else if (label == Left_Pallidum) proper_label = Right_Pallidum;
else if (label == Left_Inf_Lat_Vent)
proper_label = Right_Inf_Lat_Vent;
}
break;
case Right_Hippocampus:
if (zt > 15)
{
printf
("ERROR: %s: "
"%d %d %d, tal x=%f, y=%f, *** z=%f > 15 ***\n",
cma_label_to_name(label),x,y,z,xt,yt,zt);
fflush(stdout) ;
errors++;
}
// no break (check xt)
case Right_Caudate:
case Right_Amygdala:
case Right_Putamen:
case Right_Pallidum:
case Right_Inf_Lat_Vent:
if (xt < -5)
{
printf
("ERROR: %s: "
"%d %d %d, tal *** x=%f < -5 ***, y=%f, z=%f\n",
cma_label_to_name(label), x,y,z,xt,yt,zt);
fflush(stdout) ;
errors++;
if (label == Right_Hippocampus) proper_label = Left_Hippocampus;
else if (label == Right_Caudate) proper_label = Left_Caudate;
else if (label == Right_Amygdala) proper_label = Left_Amygdala;
else if (label == Right_Putamen) proper_label = Left_Putamen;
else if (label == Right_Pallidum) proper_label = Left_Pallidum;
else if (label == Right_Inf_Lat_Vent)
proper_label = Left_Inf_Lat_Vent;
}
break;
default:
break ;
}
/*
* collect stats on positioning of structures.
* used to determine reasonable boundaries.
*/
switch (label)
{
case Left_Hippocampus:
if (xt > max_xtal_l_hippo) max_xtal_l_hippo = xt;
break;
case Left_Caudate:
if (xt > max_xtal_l_caudate) max_xtal_l_caudate = xt;
break;
case Left_Amygdala:
if (xt > max_xtal_l_amygdala) max_xtal_l_amygdala = xt;
break;
case Left_Putamen:
if (xt > max_xtal_l_putamen) max_xtal_l_putamen = xt;
break;
case Left_Pallidum:
if (xt > max_xtal_l_pallidum) max_xtal_l_pallidum = xt;
break;
case Right_Hippocampus:
if (xt < min_xtal_r_hippo) min_xtal_r_hippo = xt;
break;
case Right_Caudate:
if (xt < min_xtal_r_caudate) min_xtal_r_caudate = xt;
break;
case Right_Amygdala:
if (xt < min_xtal_r_amygdala) min_xtal_r_amygdala = xt;
break;
case Right_Putamen:
if (xt < min_xtal_r_putamen) min_xtal_r_putamen = xt;
break;
case Right_Pallidum:
if (xt < min_xtal_r_pallidum) min_xtal_r_pallidum = xt;
break;
default:
break ;
}
}
/*
* if -check_and_fix is being used, then mod our fixed volume
*/
if (do_fix_badsubjs && (label != proper_label))
{
MRIsetVoxVal(mri_fixed, x, y, z, 0, proper_label) ;
}
}
}
}
// stats used to determine optimal boundaries
printf("max_xtal_l_hippo = %4.1f\n",max_xtal_l_hippo);
printf("max_xtal_l_caudate = %4.1f\n",max_xtal_l_caudate);
printf("max_xtal_l_amygdala = %4.1f\n",max_xtal_l_amygdala);
printf("max_xtal_l_putamen = %4.1f\n",max_xtal_l_putamen);
printf("max_xtal_l_pallidum = %4.1f\n",max_xtal_l_pallidum);
printf("min_xtal_r_hippo = %4.1f\n",min_xtal_r_hippo);
printf("min_xtal_r_caudate = %4.1f\n",min_xtal_r_caudate);
printf("min_xtal_r_amygdala = %4.1f\n",min_xtal_r_amygdala);
printf("min_xtal_r_putamen = %4.1f\n",min_xtal_r_putamen);
printf("min_xtal_r_pallidum = %4.1f\n",min_xtal_r_pallidum);
if ( do_fix_badsubjs && errors)
{
char fname[STRLEN];
sprintf(fname, "%s/%s/mri/seg_fixed.mgz", subjects_dir, subject_name);
printf("Writing corrected volume to %s\n",fname);
MRIwrite(mri_fixed,fname);
MRIfree(&mri_fixed);
}
fflush(stdout);
return(errors) ;
}
