int main (int argc,char *argv[])
{/* Main */
static char FuncName[]={"SurfToSurf"};
SUMA_GENERIC_PROG_OPTIONS_STRUCT *Opt;
SUMA_GENERIC_ARGV_PARSE *ps=NULL;
SUMA_SurfaceObject *SO1=NULL, *SO2 = NULL;
SUMA_SurfSpecFile *Spec = NULL;
SUMA_M2M_STRUCT *M2M = NULL;
int N_Spec=0, *nodeind = NULL, N_nodeind, icol, i, j;
MRI_IMAGE *im = NULL, *im_data=NULL;
int nvec=0, ncol=0, nvec_data=0, ncol_data=0, Nchar=0;
float *far = NULL, *far_data=NULL, *dt = NULL, *projdir=NULL;
char *outname = NULL, *s=NULL, sbuf[100];
void *SO_name = NULL;
FILE *outptr=NULL;
SUMA_Boolean exists = NOPE;
SUMA_INDEXING_ORDER d_order = SUMA_NO_ORDER;
SUMA_STRING *SS=NULL;
SUMA_Boolean LocalHead = NOPE;
SUMA_STANDALONE_INIT;
SUMA_mainENTRY;
/* Allocate space for DO structure */
SUMAg_DOv = SUMA_Alloc_DisplayObject_Struct (SUMA_MAX_DISPLAYABLE_OBJECTS);
ps = SUMA_Parse_IO_Args(argc, argv, "-i;-t;-spec;-s;-sv;-o;");
Opt = SUMA_SurfToSurf_ParseInput (argv, argc, ps);
if (argc < 2) {
SUMA_S_Err("Too few options");
usage_SurfToSurf(ps, 0);
exit (1);
}
/* if output surface requested, check on pre-existing file */
if (ps->o_N_surfnames) {
SO_name = SUMA_Prefix2SurfaceName(ps->o_surfnames[0],
NULL, NULL, ps->o_FT[0], &exists);
if (exists) {
fprintf(SUMA_STDERR,
"Error %s:\nOutput file(s) %s* on disk.\n"
"Will not overwrite.\n", FuncName, ps->o_surfnames[0]);
exit(1);
}
}
if (Opt->debug > 2) LocalHead = YUP;
outname = SUMA_append_extension(Opt->out_prefix,".1D");
if (SUMA_filexists(outname) && !THD_ok_overwrite()) {
fprintf(SUMA_STDERR,"Output file %s exists.\n", outname);
exit(1);
}
/* Load the surfaces from command line*/
Spec = SUMA_IO_args_2_spec(ps, &N_Spec);
if (N_Spec != 1) {
SUMA_S_Err( "Multiple spec at input.\n"
"Do not mix surface input types together\n");
exit(1);
}
if (Spec->N_Surfs != 2) {
SUMA_S_Err("2 surfaces expected.");
exit(1);
}
SO1 = SUMA_Load_Spec_Surf(Spec, 0, ps->sv[0], 0);
if (!SO1) {
fprintf (SUMA_STDERR,"Error %s:\n"
"Failed to find surface\n"
"in spec file. \n",
FuncName );
exit(1);
}
if (!SUMA_SurfaceMetrics(SO1, "EdgeList|MemberFace", NULL)) {
SUMA_SL_Err("Failed to create edge list for SO1");
exit(1);
}
if (Opt->fix_winding) {
int orient, trouble;
if (LocalHead)
fprintf(SUMA_STDERR,
"%s: Making sure S1 is consistently orientated\n", FuncName);
if (!SUMA_MakeConsistent (SO1->FaceSetList, SO1->N_FaceSet,
SO1->EL, Opt->debug, &trouble)) {
SUMA_SL_Err("Failed in SUMA_MakeConsistent");
}
if (trouble && LocalHead) {
fprintf(SUMA_STDERR,
"%s: trouble value of %d from SUMA_MakeConsistent.\n"
"Inconsistencies were found and corrected unless \n"
"stderr output messages from SUMA_MakeConsistent\n"
"indicate otherwise.\n", FuncName, trouble);
}
if (LocalHead)
fprintf(SUMA_STDERR,"%s: Checking orientation.\n", FuncName);
orient = SUMA_OrientTriangles (SO1->NodeList, SO1->N_Node,
SO1->FaceSetList, SO1->N_FaceSet,
1, 0, NULL, NULL);
if (orient < 0) {
/* flipping was done, dump the edge list since it is not
automatically updated (should do that in function,
just like in SUMA_MakeConsistent, shame on you)
If you revisit this section, use the newer:
SUMA_OrientSOTriangles
*/
if (SO1->EL) SUMA_free_Edge_List(SO1->EL); SO1->EL = NULL;
if (!SUMA_SurfaceMetrics(SO1, "EdgeList", NULL)) {
SUMA_SL_Err("Failed to create edge list for SO1"); exit(1);
}
/* free normals, new ones needed (Normals should be flipped inside of
SUMA_OrientTriangles! (just like in SUMA_MakeConsistent) ) */
if (SO1->NodeNormList) SUMA_free(SO1->NodeNormList);
SO1->NodeNormList = NULL;
if (SO1->FaceNormList) SUMA_free(SO1->FaceNormList);
SO1->FaceNormList = NULL;
}
if (!orient) {
fprintf(SUMA_STDERR,
"Error %s:\nFailed in SUMA_OrientTriangles\n", FuncName);
}
if (LocalHead) {
if (orient < 0) { SUMA_SL_Note("S1 was reoriented"); }
else { SUMA_SL_Note("S1 was properly oriented"); }
}
}
if (!SO1->NodeNormList || !SO1->FaceNormList) {
SUMA_LH("Node Normals"); SUMA_RECOMPUTE_NORMALS(SO1);
}
if (Opt->NodeDbg >= SO1->N_Node) {
SUMA_SL_Warn( "node_debug index is larger than number "
"of nodes in surface, ignoring -node_debug.");
Opt->NodeDbg = -1;
}
SO2 = SUMA_Load_Spec_Surf(Spec, 1, ps->sv[1], 0);
if (!SO2) {
fprintf (SUMA_STDERR,"Error %s:\n"
"Failed to find surface\n"
"in spec file. \n",
FuncName );
exit(1);
}
if (!SUMA_SurfaceMetrics(SO2, "EdgeList|MemberFace", NULL)) {
SUMA_SL_Err("Failed to create edge list for SO2"); exit(1);
}
if (!SO2->NodeNormList || !SO2->FaceNormList) {
SUMA_LH("Node Normals"); SUMA_RECOMPUTE_NORMALS(SO2);
}
if (LocalHead) {
SUMA_LH("Surf1");
SUMA_Print_Surface_Object(SO1, NULL);
SUMA_LH("Surf2");
SUMA_Print_Surface_Object(SO2, NULL);
}
/* a select list of nodes? */
nodeind = NULL; N_nodeind = 0;
if (Opt->in_nodeindices) {
im = mri_read_1D(Opt->in_nodeindices);
if (!im) { SUMA_SL_Err("Failed to read 1D file of node indices"); exit(1);}
far = MRI_FLOAT_PTR(im);
N_nodeind = nvec = im->nx;
ncol = im->ny;
if (ncol != 1) {
SUMA_SL_Err("More than one column in node index input file."); exit(1);
}
nodeind = (int *)SUMA_calloc(nvec, sizeof(int));
if (!nodeind) { SUMA_SL_Crit("Failed to allocate"); exit(1); }
for (i=0;i<nvec;++i) {
nodeind[i] = (int)far[i];
if (nodeind[i] < 0 || nodeind[i] >= SO1->N_Node) {
fprintf(SUMA_STDERR,
"Error %s:\n"
"A node index of %d was found in input file %s, entry %d.\n"
"Acceptable indices are positive and less than %d\n",
FuncName, nodeind[i], Opt->in_nodeindices, i, SO1->N_Node);
exit(1);
}
}
mri_free(im); im = NULL; /* done with that baby */
}
/* a preset directions vector ?*/
projdir = NULL;
if (Opt->in_1D) {
im = mri_read_1D(Opt->in_1D);
if (!im) {
SUMA_SL_Err("Failed to read 1D file of projection directions"); exit(1);
}
far = MRI_FLOAT_PTR(im);
if (im->ny != 3) {
SUMA_SL_Err("Need three columns in projection directions file.");
exit(1);
}
if (im->nx != SO1->N_Node) {
fprintf(SUMA_STDERR,
"Error %s: You must have a direction for each node in SO1.\n"
"%d directions found but SO1 has %d nodes.\n",
FuncName, im->nx, SO1->N_Node);
exit(1);
}
/* change to row major major and make it match nodeind */
projdir = (float *)SUMA_calloc(SO1->N_Node*3, sizeof(float));
if (!projdir) { SUMA_SL_Crit("Failed to allocate"); exit(1); }
for (i=0; i<SO1->N_Node; ++i) {
projdir[3*i ] = far[i ];
projdir[3*i+1] = far[i+ SO1->N_Node];
projdir[3*i+2] = far[i+2*SO1->N_Node];
}
mri_free(im); im = NULL; /* done with that baby */
}
if (SO_name) {
/* user is interpolating surface coords, check on other input insanity */
if (nodeind) {
fprintf( SUMA_STDERR,
"Error %s: You cannot combine "
"option -o_TYPE with -node_indices", FuncName);
exit(1);
}
if (Opt->in_name) {
fprintf(SUMA_STDERR,
"Error %s: You cannot combine option -o_TYPE with -data",
FuncName);
exit(1);
}
}
/* a 1D file containing data, or Data parameter (for XYZ)? */
if (Opt->Data > 0) {
if (Opt->in_name) {
/* When you are ready to work with dsets, you should
checkout the function morphDsetToStd. It uses M2M */
im_data = mri_read_1D(Opt->in_name);
if (!im_data) {
SUMA_SL_Err("Failed to read 1D file of data"); exit(1);}
far_data = MRI_FLOAT_PTR(im_data);
nvec_data = im_data->nx;
ncol_data = im_data->ny;
if (nvec_data != SO2->N_Node) {
SUMA_SL_Err("Your data file must have one row "
"for each node in surface 2.\n"); exit(1);
}
d_order = SUMA_COLUMN_MAJOR;
} else {
im_data = NULL;
far_data = SO2->NodeList;
nvec_data = SO2->N_Node;
ncol_data = 3;
d_order = SUMA_ROW_MAJOR;
}
} else {
/* just -dset */
}
if (!Opt->s) {
SUMA_LH("Going for the mapping of SO1 --> SO2");
M2M = SUMA_GetM2M_NN( SO1, SO2, nodeind, N_nodeind,
projdir, 0, Opt->NodeDbg, Opt->iopt);
SUMA_S_Notev("Saving M2M into %s\n\n",
Opt->out_prefix);
if (!(SUMA_Save_M2M(Opt->out_prefix, M2M))) {
SUMA_S_Err("Failed to save M2M");
exit(1);
}
} else {
SUMA_S_Notev("Reusing mapping of SO1 --> SO2 from %s\n\n",
Opt->s);
if (!(M2M = SUMA_Load_M2M(Opt->s))) {
SUMA_S_Errv("Failed to load %s\n", Opt->s);
exit(1);
}
}
/* Now show the mapping results for a debug node ? */
if (Opt->NodeDbg >= 0) {
char *s = NULL;
s = SUMA_M2M_node_Info(M2M, Opt->NodeDbg);
fprintf(SUMA_STDERR,"%s: Debug for node %d ([%f, %f, %f])of SO1:\n%s\n\n",
FuncName, Opt->NodeDbg,
SO1->NodeList[3*Opt->NodeDbg],
SO1->NodeList[3*Opt->NodeDbg+1],
SO1->NodeList[3*Opt->NodeDbg+2],
s);
SUMA_free(s); s = NULL;
}
/* Now please do the interpolation */
if (Opt->Data > 0) {
if (Opt->NearestNode > 1)
dt = SUMA_M2M_interpolate( M2M, far_data, ncol_data,
nvec_data, d_order, 0 );
else if (Opt->NearestNode == 1)
dt = SUMA_M2M_interpolate( M2M, far_data, ncol_data,
nvec_data, d_order, 1 );
if (!dt) {
SUMA_SL_Err("Failed to interpolate");
exit(1);
}
} else if (Opt->Data < 0) {
SUMA_DSET *dset=NULL, *dseto=NULL;
char *oname=NULL, *uname=NULL, *s1=NULL, *s2=NULL;
int iform=SUMA_NO_DSET_FORMAT;
if (Opt->NodeDbg>= 0) {
SUMA_S_Notev("Processing dset %s\n", Opt->in_name);
}
iform = SUMA_NO_DSET_FORMAT;
if (!(dset = SUMA_LoadDset_s (Opt->in_name, &iform, 0))) {
SUMA_S_Errv("Failed to load %s\n", Opt->in_name);
exit(1);
}
if (!(dseto = SUMA_morphDsetToStd ( dset, M2M,
Opt->NearestNode == 1 ? 1:0))) {
SUMA_S_Errv("Failed to map %s\n", Opt->in_name);
exit(1);
}
s1 = SUMA_append_string(
SUMA_FnameGet(Opt->in_name,"pa", SUMAg_CF->cwd),
Opt->out_prefix);
s2 = SUMA_RemoveDsetExtension_s(
SUMA_FnameGet(Opt->in_name,"l",SUMAg_CF->cwd),
SUMA_NO_DSET_FORMAT);
uname = SUMA_append_extension(s1,s2);
SUMA_free(s1); SUMA_free(s2);
oname = SUMA_WriteDset_s (uname, dseto, Opt->oform, 1, 1);
if (Opt->NodeDbg>= 0) SUMA_S_Notev("Wrote %s\n", oname);
if (oname) SUMA_free(oname); oname=NULL;
if (uname) SUMA_free(uname); oname=NULL;
if (dseto) SUMA_FreeDset(dseto); dseto = NULL;
if (dset) SUMA_FreeDset(dset); dset = NULL;
}
SUMA_LH("Forming the remaining output");
outptr = fopen(outname,"w");
if (!outptr) {
SUMA_SL_Err("Failed to open file for output.\n");
exit(1);
}
/* first create the header of the output */
SS = SUMA_StringAppend(NULL, NULL);
SS = SUMA_StringAppend_va(SS,
"#Mapping from nodes on surf 1 (S1) to nodes on surf 2 (S2)\n"
"# Surf 1 is labeled %s, idcode:%s\n"
"# Surf 2 is labeled %s, idcode:%s\n",
SO1->Label, SO1->idcode_str, SO2->Label, SO2->idcode_str);
icol = 0;
SS = SUMA_StringAppend_va(SS, "#Col. %d:\n"
"# S1n (or nj): Index of node on S1\n"
, icol);
++icol;
if (Opt->NearestNode > 1) {
SS = SUMA_StringAppend_va(SS,
"#Col. %d..%d:\n"
"# S2ne_S1n: Indices of %d nodes on S2 \n"
"# that are closest neighbors of nj.\n"
"# The first index is that of the node on S2 that is closest \n"
"# to nj. If -1 then these values should be ignored because\n"
"# in such cases, nj's projection failed.\n"
, icol, icol+Opt->NearestNode-1, Opt->NearestNode);
icol += Opt->NearestNode;
SS = SUMA_StringAppend_va(SS,
"#Col. %d..%d:\n"
"# S2we_S1n: Weights assigned to nodes on surf 2 (S2) \n"
"# that are closest neighbors of nj.\n"
, icol, icol+Opt->NearestNode-1, Opt->NearestNode);
icol += Opt->NearestNode;
} else if (Opt->NearestNode == 1) {
SS = SUMA_StringAppend_va(SS,
"#Col. %d:\n"
"# S2ne_S1n: Index of the node on S2 (label:%s idcode:%s)\n"
"# that is the closest neighbor of nj.\n"
"# If -1 then this value should be ignored because\n"
"# nj's projection failed.\n"
, icol, SO2->Label, SO2->idcode_str);
++icol;
}
if (Opt->NearestTriangle) {
SS = SUMA_StringAppend_va(SS,
"#Col. %d:\n"
"# S2t_S1n: Index of the S2 triangle that hosts node nj on S1.\n"
"# In other words, nj's closest projection onto S2 falls on \n"
"# triangle S2t_S1n\n"
"# If -1 then this value should be ignored because \n"
"# nj's projection failed.\n"
, icol);
++icol;
}
if (Opt->ProjectionOnMesh) {
SS = SUMA_StringAppend_va(SS,
"#Col. %d..%d:\n"
"# S2p_S1n: Coordinates of projection of nj onto S2\n"
, icol, icol+2);
icol += 3;
}
if (Opt->DistanceToMesh) {
SS = SUMA_StringAppend_va(SS,
"#Col. %d:\n"
"# Closest distance from nj to S2\n"
, icol);
++icol;
}
if (Opt->NearestNodeCoords) {
SS = SUMA_StringAppend_va(SS,
"#Col. %d .. %d:\n"
"# X Y Z coords of nearest node\n"
, icol, icol+2);
icol += 3;
}
if (Opt->Data > 0) {
if (!Opt->in_name) {
SS = SUMA_StringAppend_va(SS,
"#Col. %d..%d:\n"
"# Interpolation using XYZ coordinates of S2 nodes that neighbor nj\n"
"# (same as coordinates of node's projection onto triangle in S2, \n"
"# if using barycentric interpolation)\n"
, icol, icol+2);
icol += 3;
} else {
SS = SUMA_StringAppend_va(SS,
"#Col. %d..%d:\n"
"# Interpolation of data at nodes on S2 that neighbor nj\n"
"# Data obtained from %s\n"
, icol, icol+ncol_data-1, Opt->in_name); icol += ncol_data;
}
}
s = SUMA_HistString("SurfToSurf", argc, argv, NULL);
SS = SUMA_StringAppend_va(SS,
"#History:\n"
"#%s\n", s); SUMA_free(s); s = NULL;
SUMA_SS2S(SS,s);
fprintf(outptr,"%s\n",s); SUMA_free(s); s = NULL;
/* put headers atop columns */
Nchar = 6; /* if you change this number you'll need to fix formats below */
for (i=0; i<icol; ++i) {
sprintf(sbuf,"#%s", MV_format_fval2(i, Nchar -1));
fprintf(outptr,"%6s ", sbuf);
}
fprintf(outptr,"\n");
/* Now put in the values, make sure you parallel columns above! */
for (i=0; i<M2M->M1Nn; ++i) {
fprintf(outptr,"%6s ", MV_format_fval2(M2M->M1n[i], Nchar));
if (Opt->NearestNode > 0) {
for (j=0; j<Opt->NearestNode; ++j) {
if (j < M2M->M2Nne_M1n[i])
fprintf(outptr,"%6s ",
MV_format_fval2(M2M->M2ne_M1n[i][j], Nchar));
else fprintf(outptr,"%6s ", "-1");
} /* Neighboring nodes */
}
if (Opt->NearestNode > 1) { /* add the weights */
for (j=0; j<Opt->NearestNode; ++j) {
if (j < M2M->M2Nne_M1n[i])
fprintf(outptr,"%6s ",
MV_format_fval2(M2M->M2we_M1n[i][j], Nchar));
else fprintf(outptr,"%6s ", "0.0");
}
}
if (Opt->NearestTriangle) {
fprintf(outptr,"%6s ", MV_format_fval2(M2M->M2t_M1n[i], Nchar));
}
if (Opt->ProjectionOnMesh) {
fprintf(outptr,"%6s ", MV_format_fval2(M2M->M2p_M1n[3*i], Nchar));
fprintf(outptr,"%6s ", MV_format_fval2(M2M->M2p_M1n[3*i+1], Nchar));
fprintf(outptr,"%6s ", MV_format_fval2(M2M->M2p_M1n[3*i+2], Nchar));
}
if (Opt->DistanceToMesh) {
fprintf(outptr,"%6s ", MV_format_fval2(M2M->PD[i], Nchar));
}
if (Opt->NearestNodeCoords) {
float x=0.0,y=0.0,z=0.0;
int n = M2M->M2ne_M1n[i][0];
if (n>0) {
n = n * SO2->NodeDim;
x = SO2->NodeList[n];
y = SO2->NodeList[n+1];
z = SO2->NodeList[n+2];
}
fprintf(outptr,"%6s ", MV_format_fval2(x, Nchar));
fprintf(outptr,"%6s ", MV_format_fval2(y, Nchar));
fprintf(outptr,"%6s ", MV_format_fval2(z, Nchar));
}
if (dt && Opt->Data > 0) {
if (!Opt->in_name) {
fprintf(outptr,"%6s ", MV_format_fval2(dt[3*i], Nchar));
fprintf(outptr,"%6s ", MV_format_fval2(dt[3*i+1], Nchar));
fprintf(outptr,"%6s ", MV_format_fval2(dt[3*i+2], Nchar));
} else { /* Column major business */
for (j=0; j<ncol_data; ++j) {
fprintf(outptr,"%6s ",
MV_format_fval2(dt[i+j*M2M->M1Nn], Nchar)); }
}
}
fprintf(outptr,"\n");
}
/* do they want an output surface ? */
if (SO_name) {
float *tmpfv = NULL;
SUMA_LH("Writing surface");
tmpfv = SO1->NodeList;
SO1->NodeList = dt;
if (!SUMA_Save_Surface_Object (SO_name, SO1,
ps->o_FT[0], ps->o_FF[0], NULL)) {
SUMA_S_Err("Failed to write surface object.\n");
exit (1);
}
SO1->NodeList = tmpfv; tmpfv = NULL;
}
if (N_Spec) {
int k=0;
for (k=0; k<N_Spec; ++k) {
if (!SUMA_FreeSpecFields(&(Spec[k]))) {
SUMA_S_Err("Failed to free spec fields");
}
}
SUMA_free(Spec); Spec = NULL; N_Spec = 0;
}
if (projdir) SUMA_free(projdir); projdir = NULL;
if (SO_name) SUMA_free(SO_name); SO_name = NULL;
if (outptr) fclose(outptr); outptr = NULL;
if (dt) SUMA_free(dt); dt = NULL;
if (s) SUMA_free(s); s = NULL;
if (im_data) mri_free(im_data); im_data = NULL; /* done with the data */
if (nodeind) SUMA_free(nodeind); nodeind = NULL;
if (M2M) M2M = SUMA_FreeM2M(M2M);
if (SO1) SUMA_Free_Surface_Object(SO1); SO1 = NULL;
if (SO2) SUMA_Free_Surface_Object(SO2); SO2 = NULL;
if (Spec) SUMA_free(Spec); Spec = NULL;
if (ps) SUMA_FreeGenericArgParse(ps); ps = NULL;
if (Opt) Opt = SUMA_Free_Generic_Prog_Options_Struct(Opt);
if (!SUMA_Free_CommonFields(SUMAg_CF)) SUMA_error_message(FuncName,"SUMAg_CF Cleanup Failed!",1);
exit(0);
}
int main(int argc, char *argv[]) {
int i,j,k,m,n,mm;
int iarg;
THD_3dim_dataset *insetTIME = NULL;
THD_3dim_dataset *MASK=NULL;
THD_3dim_dataset *ROIS=NULL;
char *prefix="NETCORR" ;
char in_name[300];
char in_mask[300];
char in_rois[300];
char OUT_grid[300];
char OUT_indiv[300];
char OUT_indiv0[300];
// int *SELROI=NULL; // if selecting subset of ROIs
// int HAVE_SELROI=0;
int NIFTI_OUT = 0;
byte ***mskd=NULL; // define mask of where time series are nonzero
byte *mskd2=NULL; // not great, but another format of mask
int HAVE_MASK=0;
int HAVE_ROIS=0;
int FISH_OUT=0;
int PART_CORR=0;
int TS_OUT=0;
int TS_LABEL=0;
int TS_INDIV=0;
int TS_WBCORR_r=0;
int TS_WBCORR_Z=0;
int *NROI_REF=NULL,*INVROI_REF=NULL;
int **ROI_LABELS_REF=NULL, **INV_LABELS_REF=NULL,**ROI_COUNT=NULL;
int ***ROI_LISTS=NULL;
double ***ROI_AVE_TS=NULL; // double because of GSL
float ***Corr_Matr=NULL;
float ***PCorr_Matr=NULL, ***PBCorr_Matr=NULL;
int Nvox=-1; // tot number vox
int *Dim=NULL;
int *Nlist=NULL;
Dtable *roi_dtable=NULL;
char *LabTabStr=NULL;
char ***ROI_STR_LABELS=NULL;
// for niml.dset -> graph viewing in SUMA
char ***gdset_roi_names=NULL;
SUMA_DSET *gset=NULL;
float ***flat_matr=NULL;
float *xyz=NULL;
char OUT_gdset[300];
NI_group *GDSET_netngrlink=NULL;
char *NAME_gdset=NULL;
int Noutmat = 1; // num of matr to output: start with CC for sure
char **ParLab=NULL;
int FM_ctr = 0; // for counting through flatmatr entries
int OLD_LABEL=0; // ooollld style format of regions: Nnumber:Rnumber
int IGNORE_LT=0; // ignore label table
int idx = 0;
int Nmask = 0;
FILE *fout1,*fin,*fout2;
AFNI_SETUP_OMP(0) ; /* 24 Jun 2013 */
mainENTRY("3dNetCorr"); machdep();
// ****************************************************************
// ****************************************************************
// load AFNI stuff
// ****************************************************************
// ****************************************************************
// INFO_message("version: BETA");
/** scan args **/
if (argc == 1) { usage_NetCorr(1); exit(0); }
iarg = 1;
while( iarg < argc && argv[iarg][0] == '-' ){
if( strcmp(argv[iarg],"-help") == 0 ||
strcmp(argv[iarg],"-h") == 0 ) {
usage_NetCorr(strlen(argv[iarg])>3 ? 2:1);
exit(0);
}
if( strcmp(argv[iarg],"-prefix") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-prefix'");
prefix = strdup(argv[iarg]) ;
if( !THD_filename_ok(prefix) )
ERROR_exit("Illegal name after '-prefix'");
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-inset") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-input'");
sprintf(in_name,"%s", argv[iarg]);
insetTIME = THD_open_dataset(in_name) ;
if( (insetTIME == NULL ))
ERROR_exit("Can't open time series dataset '%s'.",in_name);
// just 0th time point for output...
Dim = (int *)calloc(4,sizeof(int));
DSET_load(insetTIME); CHECK_LOAD_ERROR(insetTIME);
Nvox = DSET_NVOX(insetTIME) ;
Dim[0] = DSET_NX(insetTIME); Dim[1] = DSET_NY(insetTIME);
Dim[2] = DSET_NZ(insetTIME); Dim[3]= DSET_NVALS(insetTIME);
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-mask") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-mask'");
HAVE_MASK= 1;
sprintf(in_mask,"%s", argv[iarg]);
MASK = THD_open_dataset(in_mask) ;
if( (MASK == NULL ))
ERROR_exit("Can't open time series dataset '%s'.",in_mask);
DSET_load(MASK); CHECK_LOAD_ERROR(MASK);
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-in_rois") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-in_rois'");
sprintf(in_rois,"%s", argv[iarg]);
ROIS = THD_open_dataset(in_rois) ;
if( (ROIS == NULL ))
ERROR_exit("Can't open time series dataset '%s'.",in_rois);
DSET_load(ROIS); CHECK_LOAD_ERROR(ROIS);
HAVE_ROIS=DSET_NVALS(ROIS); //number of subbricks
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-fish_z") == 0) {
FISH_OUT=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-nifti") == 0) {
NIFTI_OUT=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-part_corr") == 0) {
PART_CORR=2; // because we calculate two matrices here
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-ts_out") == 0) {
TS_OUT=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-ts_label") == 0) {
TS_LABEL=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-ts_indiv") == 0) {
TS_INDIV=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-ts_wb_corr") == 0) {
TS_WBCORR_r=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-ts_wb_Z") == 0) {
TS_WBCORR_Z=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-old_labels") == 0) {
OLD_LABEL=1;
iarg++ ; continue ;
}
if( strcmp(argv[iarg],"-ignore_LT") == 0) {
IGNORE_LT=1;
iarg++ ; continue ;
}
/* if( strcmp(argv[iarg],"-sel_roi") == 0 ){
iarg++ ; if( iarg >= argc )
ERROR_exit("Need argument after '-in_rois'");
SELROI = (int *)calloc(MAX_SELROI,sizeof(int));
if( (fin = fopen(argv[iarg], "r")) == NULL) {
fprintf(stderr, "Error opening file %s.",argv[iarg]);
exit(1);
}
idx=0;
while( !feof(fin) && (idx<MAX_SELROI-1) ){
fscanf(fin, "%d",&SELROI[idx]);
fscanf(fin," ");
idx++;
}
HAVE_SELROI=idx;
printf("HAVE_SELROI=%d\n",HAVE_SELROI);
if(HAVE_SELROI<=0) {
ERROR_message("Error reading in `-sel_roi'-- appears to have no ROIs listed.\n");
exit(1);
}
iarg++ ; continue ;
}*/
ERROR_message("Bad option '%s'\n",argv[iarg]) ;
suggest_best_prog_option(argv[0], argv[iarg]);
exit(1);
}
INFO_message("Reading in.");
if( !TS_OUT && TS_LABEL) {
ERROR_message("with '-ts_label', you also need '-ts_out'.\n");
exit(1);
}
if (iarg < 3) {
ERROR_message("Too few options. Try -help for details.\n");
exit(1);
}
if(!HAVE_ROIS) {
ERROR_message("Need to load ROIs with >=1 subbrick...\n");
exit(1);
}
if(Nvox != DSET_NVOX(ROIS)) {
ERROR_message("Data sets of `-inset' and `in_rois' have "
"different numbers of voxels per brik!\n");
exit(1);
}
if( (HAVE_MASK>0) && (Nvox != DSET_NVOX(MASK)) ) {
ERROR_message("Data sets of `-inset' and `mask' have "
"different numbers of voxels per brik!\n");
exit(1);
}
// ****************************************************************
// ****************************************************************
// make storage
// ****************************************************************
// ****************************************************************
Nlist = (int *)calloc(1,sizeof(int));
mskd2 = (byte *)calloc(Nvox,sizeof(byte));
mskd = (byte ***) calloc( Dim[0], sizeof(byte **) );
for ( i = 0 ; i < Dim[0] ; i++ )
mskd[i] = (byte **) calloc( Dim[1], sizeof(byte *) );
for ( i = 0 ; i < Dim[0] ; i++ )
for ( j = 0 ; j < Dim[1] ; j++ )
mskd[i][j] = (byte *) calloc( Dim[2], sizeof(byte) );
if( (mskd == NULL) || (Nlist == NULL) || (mskd2 == NULL)) {
fprintf(stderr, "\n\n MemAlloc failure (masks).\n\n");
exit(122);
}
// *************************************************************
// *************************************************************
// Beginning of main loops
// *************************************************************
// *************************************************************
INFO_message("Allocating...");
// go through once: define data vox, and calc rank for each
for( k=0 ; k<Dim[2] ; k++ )
for( j=0 ; j<Dim[1] ; j++ )
for( i=0 ; i<Dim[0] ; i++ ) {
if( HAVE_MASK ) {
if( THD_get_voxel(MASK,idx,0)>0 ) {
mskd[i][j][k] = 1;
mskd2[idx] = 1;
Nmask++;
}
}
else // simple automask attempt
if( fabs(THD_get_voxel(insetTIME,idx,0))+
fabs(THD_get_voxel(insetTIME,idx,1))+
fabs(THD_get_voxel(insetTIME,idx,2))+
fabs(THD_get_voxel(insetTIME,idx,3))+
fabs(THD_get_voxel(insetTIME,idx,4)) > EPS_V) {
mskd[i][j][k] = 1;
mskd2[idx] = 1;
Nmask++;
}
idx+= 1; // skip, and mskd and KW are both still 0 from calloc
}
if (HAVE_MASK) {
DSET_delete(MASK);
free(MASK);
}
// obviously, this should always be TRUE at this point...
if(HAVE_ROIS>0) {
NROI_REF = (int *)calloc(HAVE_ROIS, sizeof(int));
INVROI_REF = (int *)calloc(HAVE_ROIS, sizeof(int));
if( (NROI_REF == NULL) || (INVROI_REF == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(122);
}
for( i=0 ; i<HAVE_ROIS ; i++)
INVROI_REF[i] = (int) THD_subbrick_max(ROIS, i, 1);
ROI_LABELS_REF = calloc( HAVE_ROIS,sizeof(ROI_LABELS_REF));
for(i=0 ; i<HAVE_ROIS ; i++)
ROI_LABELS_REF[i] = calloc(INVROI_REF[i]+1,sizeof(int));
INV_LABELS_REF = calloc( HAVE_ROIS,sizeof(INV_LABELS_REF));
for(i=0 ; i<HAVE_ROIS ; i++)
INV_LABELS_REF[i] = calloc(INVROI_REF[i]+1,sizeof(int));
if( (ROI_LABELS_REF == NULL) || (INV_LABELS_REF == NULL)
) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(123);
}
INFO_message("Labelling regions internally.");
// Step 3A-2: find out the labels in the ref, organize them
// both backwards and forwards.
i = ViveLeRoi(ROIS,
ROI_LABELS_REF, // ordered list of ROILABEL ints, [1..M];
// maxval is N.
INV_LABELS_REF, // ith values at the actual input locs;
// maxval is M.
NROI_REF, // M: # of ROIs per brik
INVROI_REF); // N: max ROI label per brik
if( i != 1)
ERROR_exit("Problem loading/assigning ROI labels");
ROI_STR_LABELS = (char ***) calloc( HAVE_ROIS, sizeof(char **) );
for ( i=0 ; i<HAVE_ROIS ; i++ )
ROI_STR_LABELS[i] = (char **) calloc( NROI_REF[i]+1, sizeof(char *) );
for ( i=0 ; i<HAVE_ROIS ; i++ )
for ( j=0 ; j<NROI_REF[i]+1 ; j++ )
ROI_STR_LABELS[i][j] = (char *) calloc( 100 , sizeof(char) );
if( (ROI_STR_LABELS == NULL)) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(123);
}
// Sept 2014: Labeltable stuff
if( IGNORE_LT ) {
INFO_message("Ignoring any '-in_rois' label table (if there is one).");
}
else{
if ((ROIS->Label_Dtable = DSET_Label_Dtable(ROIS))) {
if ((LabTabStr = Dtable_to_nimlstring( DSET_Label_Dtable(ROIS),
"VALUE_LABEL_DTABLE"))) {
//fprintf(stdout,"%s", LabTabStr);
if (!(roi_dtable = Dtable_from_nimlstring(LabTabStr))) {
ERROR_exit("Could not parse labeltable.");
}
}
else {
INFO_message("No label table from '-in_rois'.");
}
}
}
i = Make_ROI_Output_Labels( ROI_STR_LABELS,
ROI_LABELS_REF,
HAVE_ROIS,
NROI_REF,
roi_dtable,
1 );//!!!opts.DUMP_with_LABELS
ROI_COUNT = calloc( HAVE_ROIS,sizeof(ROI_COUNT));
for(i=0 ; i<HAVE_ROIS ; i++)
ROI_COUNT[i] = calloc(NROI_REF[i],sizeof(int));
if( (ROI_COUNT == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(123);
}
// find num of vox per ROI
for( m=0 ; m<HAVE_ROIS ; m++ ) {
idx=0;
for( k=0 ; k<Dim[2] ; k++ )
for( j=0 ; j<Dim[1] ; j++ )
for( i=0 ; i<Dim[0] ; i++ ) {
if( (THD_get_voxel(ROIS,idx,m) > 0 ) && mskd[i][j][k] ) {
ROI_COUNT[m][INV_LABELS_REF[m][(int)
THD_get_voxel(ROIS,idx,m)]-1]++;
}
idx++;
}
}
// make list of vox per ROI
ROI_LISTS = (int ***) calloc( HAVE_ROIS, sizeof(int **) );
for ( i=0 ; i<HAVE_ROIS ; i++ )
ROI_LISTS[i] = (int **) calloc( NROI_REF[i], sizeof(int *) );
for ( i=0 ; i <HAVE_ROIS ; i++ )
for ( j=0 ; j<NROI_REF[i] ; j++ )
ROI_LISTS[i][j] = (int *) calloc( ROI_COUNT[i][j], sizeof(int) );
// make average time series per voxel
ROI_AVE_TS = (double ***) calloc( HAVE_ROIS, sizeof(double **) );
for ( i=0 ; i<HAVE_ROIS ; i++ )
ROI_AVE_TS[i] = (double **) calloc( NROI_REF[i], sizeof(double *) );
for ( i=0 ; i <HAVE_ROIS ; i++ )
for ( j=0 ; j<NROI_REF[i] ; j++ )
ROI_AVE_TS[i][j] = (double *) calloc( Dim[3], sizeof(double) );
// store corr coefs
Corr_Matr = (float ***) calloc( HAVE_ROIS, sizeof(float **) );
for ( i=0 ; i<HAVE_ROIS ; i++ )
Corr_Matr[i] = (float **) calloc( NROI_REF[i], sizeof(float *) );
for ( i=0 ; i <HAVE_ROIS ; i++ )
for ( j=0 ; j<NROI_REF[i] ; j++ )
Corr_Matr[i][j] = (float *) calloc( NROI_REF[i], sizeof(float) );
if( (ROI_LISTS == NULL) || (ROI_AVE_TS == NULL)
|| (Corr_Matr == NULL)) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(123);
}
if(PART_CORR) {
PCorr_Matr = (float ***) calloc( HAVE_ROIS, sizeof(float **) );
for ( i=0 ; i<HAVE_ROIS ; i++ )
PCorr_Matr[i] = (float **) calloc( NROI_REF[i], sizeof(float *) );
for ( i=0 ; i <HAVE_ROIS ; i++ )
for ( j=0 ; j<NROI_REF[i] ; j++ )
PCorr_Matr[i][j] = (float *) calloc( NROI_REF[i], sizeof(float));
PBCorr_Matr = (float ***) calloc( HAVE_ROIS, sizeof(float **) );
for ( i=0 ; i<HAVE_ROIS ; i++ )
PBCorr_Matr[i] = (float **) calloc( NROI_REF[i], sizeof(float *) );
for ( i=0 ; i <HAVE_ROIS ; i++ )
for ( j=0 ; j<NROI_REF[i] ; j++ )
PBCorr_Matr[i][j] = (float *) calloc( NROI_REF[i], sizeof(float));
if( (PCorr_Matr == NULL) || (PBCorr_Matr == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(123);
}
}
// reuse this to help place list indices
for( i=0 ; i<HAVE_ROIS ; i++ )
for( j=0 ; j<NROI_REF[i] ; j++ )
ROI_COUNT[i][j] = 0;
INFO_message("Getting volumes.");
for( m=0 ; m<HAVE_ROIS ; m++ ) {
idx=0;
for( k=0 ; k<Dim[2] ; k++ )
for( j=0 ; j<Dim[1] ; j++ )
for( i=0 ; i<Dim[0] ; i++ ) {
if( (THD_get_voxel(ROIS,idx,m) > 0) && mskd[i][j][k] ) {
mm = INV_LABELS_REF[m][(int) THD_get_voxel(ROIS,idx,m)]-1;
ROI_LISTS[m][mm][ROI_COUNT[m][mm]] = idx;
ROI_COUNT[m][mm]++;
}
idx++;
}
}
}
// bit of freeing
for( i=0 ; i<Dim[0] ; i++)
for( j=0 ; j<Dim[1] ; j++) {
free(mskd[i][j]);
}
for( i=0 ; i<Dim[0] ; i++) {
free(mskd[i]);
}
free(mskd);
INFO_message("Calculating average time series.");
// ROI values
for(i=0 ; i<HAVE_ROIS ; i++)
for( j=0 ; j<NROI_REF[i] ; j++ ) {
Nlist[0]=ROI_COUNT[i][j];
k = CalcAveRTS(ROI_LISTS[i][j], ROI_AVE_TS[i][j],
insetTIME, Dim, Nlist);
}
INFO_message("Calculating correlation matrix.");
if(PART_CORR)
INFO_message("... and calculating partial correlation matrix.");
for(i=0 ; i<HAVE_ROIS ; i++) {
for( j=0 ; j<NROI_REF[i] ; j++ )
for( k=j ; k<NROI_REF[i] ; k++ ) {
Corr_Matr[i][j][k] = Corr_Matr[i][k][j] = (float)
CORR_FUN(ROI_AVE_TS[i][j], ROI_AVE_TS[i][k], Dim[3]);
}
if(PART_CORR)
mm = CalcPartCorrMatr(PCorr_Matr[i], PBCorr_Matr[i],
Corr_Matr[i], NROI_REF[i]);
}
// **************************************************************
// **************************************************************
// Store and output
// **************************************************************
// **************************************************************
INFO_message("Writing output: %s ...", prefix);
// - - - - - - - - NIML prep - - - - - - - - - - - - - -
if(FISH_OUT)
Noutmat++;
if(PART_CORR)
Noutmat+=2;
ParLab = (char **)calloc(Noutmat, sizeof(char *));
for (j=0; j<Noutmat; ++j)
ParLab[j] = (char *)calloc(32, sizeof(char));
if( (ParLab == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(121);
}
// NIML output
flat_matr = (float ***) calloc( HAVE_ROIS, sizeof(float **) );
for ( i = 0 ; i < HAVE_ROIS ; i++ )
flat_matr[i] = (float **) calloc( Noutmat, sizeof(float *) );
for ( i = 0 ; i < HAVE_ROIS ; i++ )
for ( j = 0 ; j < Noutmat ; j++ )
flat_matr[i][j] = (float *) calloc( NROI_REF[i]*NROI_REF[i],
sizeof(float));
gdset_roi_names = (char ***)calloc(HAVE_ROIS, sizeof(char **));
for (i=0; i< HAVE_ROIS ; i++ ) {
gdset_roi_names[i] = (char **)calloc(NROI_REF[i], sizeof(char *));
for (j=0; j<NROI_REF[i]; ++j) {
gdset_roi_names[i][j] = (char *)calloc(32, sizeof(char));
if( OLD_LABEL )
snprintf(gdset_roi_names[i][j],31,"N%03d:R%d", i,
ROI_LABELS_REF[i][j]);
else{
snprintf(gdset_roi_names[i][j],31,"%s",
ROI_STR_LABELS[i][j+1]);
//fprintf(stderr," %s ",
// ROI_STR_LABELS[i][j+1]);
}
}
}
if( (flat_matr == NULL) || ( gdset_roi_names == NULL) ) {
fprintf(stderr, "\n\n MemAlloc failure.\n\n");
exit(14);
}
for( k=0 ; k<HAVE_ROIS ; k++) { // each netw gets own file
sprintf(OUT_grid,"%s_%03d.netcc",prefix,k); // zero counting now
if( (fout1 = fopen(OUT_grid, "w")) == NULL) {
fprintf(stderr, "Error opening file %s.",OUT_grid);
exit(19);
}
// same format as .grid files now
fprintf(fout1,"# %d # Number of network ROIs\n",NROI_REF[k]); // NROIs
fprintf(fout1,"# %d # Number of netcc matrices\n",
FISH_OUT+PART_CORR+1); // Num of params
// Sept 2014: label_table stuff
// don't need labeltable to make them, can do anyways
fprintf(fout1, "# WITH_ROI_LABELS\n");
for( i=1 ; i<NROI_REF[k] ; i++ )
fprintf(fout1," %10s \t",ROI_STR_LABELS[k][i]);
fprintf(fout1," %10s\n",ROI_STR_LABELS[k][i]);
// THIS IS FOR KNOWING WHICH MATR WE'RE AT
// it's always zero for CC; they match one-to-one with later vars
FM_ctr = 0;
ParLab[FM_ctr] = strdup("CC");
for( i=1 ; i<NROI_REF[k] ; i++ ) // labels of ROIs
fprintf(fout1," %10d \t",ROI_LABELS_REF[k][i]);// at =NROI, have '\n'
fprintf(fout1," %10d\n# %s\n",ROI_LABELS_REF[k][i],"CC");
for( i=0 ; i<NROI_REF[k] ; i++ ) {
for( j=0 ; j<NROI_REF[k]-1 ; j++ ) {// b/c we put '\n' after last one.
fprintf(fout1,"%12.4f\t",Corr_Matr[k][i][j]);
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] = Corr_Matr[k][i][j];
}
fprintf(fout1,"%12.4f\n",Corr_Matr[k][i][j]);
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] = Corr_Matr[k][i][j];
}
if(FISH_OUT) {
FM_ctr++;
ParLab[FM_ctr] = strdup("FZ");
fprintf(fout1,"# %s\n", "FZ");
for( i=0 ; i<NROI_REF[k] ; i++ ) {
for( j=0 ; j<NROI_REF[k]-1 ; j++ ) {// b/c we put '\n' after last
fprintf(fout1,"%12.4f\t",BOBatanhf(Corr_Matr[k][i][j]));
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] =
BOBatanhf(Corr_Matr[k][i][j]);
/* fprintf(fout1,"%12.4f\t",FisherZ(Corr_Matr[k][i][j]));
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] =
FisherZ(Corr_Matr[k][i][j]);*/
}
fprintf(fout1,"%12.4f\n",BOBatanhf(Corr_Matr[k][i][j]));
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] =
BOBatanhf(Corr_Matr[k][i][j]);
/*fprintf(fout1,"%12.4f\n",FisherZ(Corr_Matr[k][i][j]));
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] =
FisherZ(Corr_Matr[k][i][j]);*/
}
}
if(PART_CORR) {
FM_ctr++;
ParLab[FM_ctr] = strdup("PC");
fprintf(fout1,"# %s\n", "PC");
for( i=0 ; i<NROI_REF[k] ; i++ ) {
for( j=0 ; j<NROI_REF[k]-1 ; j++ ) {// b/c we put '\n' after last
fprintf(fout1,"%12.4f\t",PCorr_Matr[k][i][j]);
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] = PCorr_Matr[k][i][j];
}
fprintf(fout1,"%12.4f\n",PCorr_Matr[k][i][j]);
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] = PCorr_Matr[k][i][j];
}
FM_ctr++;
ParLab[FM_ctr] = strdup("PCB");
fprintf(fout1,"# %s\n", "PCB");
for( i=0 ; i<NROI_REF[k] ; i++ ) {
for( j=0 ; j<NROI_REF[k]-1 ; j++ ) {// b/c we put '\n' after last
fprintf(fout1,"%12.4f\t",PBCorr_Matr[k][i][j]);
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] = PBCorr_Matr[k][i][j];
}
fprintf(fout1,"%12.4f\n",PBCorr_Matr[k][i][j]);
flat_matr[k][FM_ctr][i*NROI_REF[k]+j] = PBCorr_Matr[k][i][j];
}
}
fclose(fout1);
// more nimling
gset = SUMA_FloatVec_to_GDSET(flat_matr[k], Noutmat,
NROI_REF[k]*NROI_REF[k],
"full", ParLab,
NULL, NULL, NULL);
if( xyz = THD_roi_cmass(ROIS, k, ROI_LABELS_REF[k]+1, NROI_REF[k]) ) {
if (!(SUMA_AddGDsetNodeListElement(gset, NULL,
xyz, NULL, NULL,
gdset_roi_names[k],
NULL, NULL,
NROI_REF[k]))) {
ERROR_message("Failed to add node list");
exit(1);
}
free(xyz);
}
else {
ERROR_message("Failed in THD_roi_cmass"); exit(1);
}
sprintf(OUT_gdset,"%s_%03d",prefix,k);
GDSET_netngrlink =
Network_link(SUMA_FnameGet( OUT_gdset, "f",NULL));
NI_add_to_group(gset->ngr, GDSET_netngrlink);
NAME_gdset = SUMA_WriteDset_ns( OUT_gdset,
gset, SUMA_ASCII_NIML, 1, 0);
if (!NAME_gdset && !SUMA_IS_DSET_STDXXX_FORMAT(SUMA_ASCII_NIML)) {
ERROR_message("Failed to write dataset."); exit(1);
} else {
if (NAME_gdset) SUMA_free(NAME_gdset); NAME_gdset = NULL;
}
SUMA_FreeDset(gset);
gset=NULL;
}
if(TS_OUT) {
for( k=0 ; k<HAVE_ROIS ; k++) { // each netw gets own file
sprintf(OUT_grid,"%s_%03d.netts",prefix,k);
if( (fout1 = fopen(OUT_grid, "w")) == NULL) {
fprintf(stderr, "Error opening file %s.",OUT_grid);
exit(19);
}
for( i=0 ; i<NROI_REF[k] ; i++ ) {
if(TS_LABEL)
fprintf(fout1,"%d\t",ROI_LABELS_REF[k][i+1]); // labels go 1...M
for( j=0 ; j<Dim[3]-1 ; j++ ) // b/c we put '\n' after last one.
fprintf(fout1,"%.3e\t",ROI_AVE_TS[k][i][j]);
fprintf(fout1,"%.3e\n",ROI_AVE_TS[k][i][j]);
}
fclose(fout1);
}
}
if( TS_INDIV ) {
for( k=0 ; k<HAVE_ROIS ; k++) { // each netw gets own file
sprintf(OUT_indiv0,"%s_%03d_INDIV", prefix, k);
mkdir(OUT_indiv0, 0777);
for( i=0 ; i<NROI_REF[k] ; i++ ) {
sprintf(OUT_indiv,"%s/ROI_%03d.netts",
OUT_indiv0,ROI_LABELS_REF[k][i+1]);
if( (fout2 = fopen(OUT_indiv, "w")) == NULL) {
fprintf(stderr, "\nError opening file '%s'.\n",OUT_indiv);
exit(19);
}
for( j=0 ; j<Dim[3]-1 ; j++ ) // b/c we put '\n' after last one.
fprintf(fout2,"%.3e\t",ROI_AVE_TS[k][i][j]);
fprintf(fout2,"%.3e\n",ROI_AVE_TS[k][i][j]);
fclose(fout2);
}
}
}
if( TS_WBCORR_r || TS_WBCORR_Z ) {
INFO_message("Starting whole brain correlations.");
i = WB_netw_corr( TS_WBCORR_r,
TS_WBCORR_Z,
HAVE_ROIS,
prefix,
NIFTI_OUT,
NROI_REF,
Dim,
ROI_AVE_TS,
ROI_LABELS_REF,
insetTIME,
mskd2,
Nmask,
argc,
argv);
}
// ************************************************************
// ************************************************************
// Freeing
// ************************************************************
// ************************************************************
DSET_delete(ROIS);
free(ROIS);
for ( i = 0 ; i < HAVE_ROIS ; i++ ) {
for (j = 0; j < NROI_REF[i]; ++j)
free(gdset_roi_names[i][j]);
free(gdset_roi_names[i]);
}
free(gdset_roi_names);
for ( i = 0 ; i < HAVE_ROIS ; i++ )
for ( j = 0 ; j < Noutmat ; j++ )
free(flat_matr[i][j]);
for ( i = 0 ; i < HAVE_ROIS ; i++ )
free(flat_matr[i]);
free(flat_matr);
for( i=0 ; i<Noutmat ; i++)
free(ParLab[i]);
free(ParLab);
if(LabTabStr)
free(LabTabStr);
if(roi_dtable)
free(roi_dtable);
for ( i=0 ; i<HAVE_ROIS ; i++ )
for ( j=0 ; j<NROI_REF[i]+1 ; j++ )
free(ROI_STR_LABELS[i][j]);
for ( i=0 ; i<HAVE_ROIS ; i++ )
free(ROI_STR_LABELS[i]);
free(ROI_STR_LABELS);
DSET_delete(insetTIME);
free(insetTIME);
free(mskd2);
free(Nlist);
free(Dim); // need to free last because it's used for other arrays...
free(prefix);
// if(HAVE_SELROI)
// free(SELROI);
if(HAVE_ROIS >0) {
for( i=0 ; i<HAVE_ROIS ; i++) {
for( j=0 ; j<NROI_REF[i] ; j++) {
free(ROI_LISTS[i][j]);
free(ROI_AVE_TS[i][j]);
free(Corr_Matr[i][j]);
if(PART_CORR) {
free(PCorr_Matr[i][j]);
free(PBCorr_Matr[i][j]);
}
}
free(ROI_LISTS[i]);
free(ROI_AVE_TS[i]);
free(Corr_Matr[i]);
if(PART_CORR){
free(PCorr_Matr[i]);
free(PBCorr_Matr[i]);
}
free(ROI_LABELS_REF[i]);
free(INV_LABELS_REF[i]);
free(ROI_COUNT[i]);
}
free(ROI_LISTS);
free(ROI_AVE_TS);
free(Corr_Matr);
if(PART_CORR) {
free(PCorr_Matr);
free(PBCorr_Matr);
}
free(ROI_LABELS_REF);
free(INV_LABELS_REF);
free(ROI_COUNT);
free(NROI_REF);
free(INVROI_REF);
}
return 0;
}
