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I am running babyAFQ_demo and trying to run a this cpp file using mex in MATLAB on my Mac, and receiving the error above. I have given the function readFileNifti.c below:
It seems as that I need to edit/add to the mexFunction. However, I don't know how to fix this. Any solutions would be appreciated!
/*
* Simple Matlab mex wrapper for NIFTI-1 reference code.
*
* To compile on most unices (maybe BSD/OS-X?) and windows:
* mex readFileNifti.c nifti1_io.c ../zlib/znzlib.c ../zlib/adler32.c ../zlib/compress.c ../zlib/crc32.c ../zlib/deflate.c ../zlib/gzio.c ../zlib/infback.c ../zlib/inffast.c ../zlib/inflate.c ../zlib/inftrees.c ../zlib/trees.c ../zlib/zutil.c
*
* OLD COMPILE INSTRUCTIONS
* mex readFileNifti.c nifti1_io.c znzlib.c zlib/adler32.c zlib/compress.c zlib/crc32.c zlib/deflate.c zlib/gzio.c zlib/infback.c zlib/inffast.c zlib/inflate.c zlib/inftrees.c zlib/trees.c zlib/zutil.c
* mex writeFileNifti.c nifti1_io.c znzlib.c zlib/adler32.c zlib/compress.c zlib/crc32.c zlib/deflate.c zlib/gzio.c zlib/infback.c zlib/inffast.c zlib/inflate.c zlib/inftrees.c zlib/trees.c zlib/zutil.c
*
* OLD COMPILE INSTRUCTIONS:
* On 32-bit Windows, try:
* mex -D_WINDOWS_ -I./win32 readFileNifti.c nifti1_io.c znzlib.c ./win32/zlib.lib
* On 64-bit Windows, try:
* mex -D_WINDOWS_ -I./win64 readFileNifti.c nifti1_io.c znzlib.c ./win64/zlib.lib
* On Cygwin/gnumex, try:
* mex readFileNifti.c nifti1_io.c znzlib.c -Ic:\PATHTOZLIBINCLUDE c:\PATHTOZLIB\libz.a
* On Linux, try:
* mex readFileNifti.c nifti1_io.c znzlib.c
* or:
* mex readFileNifti.c nifti1_io.c znzlib.c /usr/local/matlab/r2007a/bin/glnx86/libz.so
* or:
* mex readFileNifti.c nifti1_io.c znzlib.c /usr/local/matlab/r2007a/bin/glnxa64/libz.so
*
* Testing:
* ni=readFileNifti('/biac3/wandell5/data/relaxometry/rfd_090416/trilin2mms/T1.nii.gz');
* showMontage(ni.data)
*
*
* HISTORY:
*
* Sometime in 2006? Bob Dougherty (bobd@stanford.edu) wrote it.
*
* 2007.07.18 RFD: changed the code so that the returned qto/sto transforms are
* one-indexed rather than zero-indexed. With this change, the qto/sto transforms
* now map to and from Matlab's one-indexed voxel volume rather than the zero-indexed
* volume of the NIFTI spec. This allows us to keep the data on disk in the
* NIFTI-compliant zero-indexed form while allowing convenient transforms for
* our one-indexed Matlab world.
*
* 2009.03.24 RFD: update nifti reference code to latest and added support for RGB data.
*
* 2009.09.24 RFD: fixed qto X-origin off-by-one error with left-right flipped data (ie. qfac<0).
*
* 2010.01.26 RFD: copied zlib code source code so that we can build zlib
* functions directly rather than trying to include a zlib library. This
* makes compiling easier, especially when the matlab and system zlib
* versions are very different. Also fixed a bug that caused core-dumps on
* newer compilers-- a non-existant field ("datatype") was being set.
*
*/
#include "mex.h"
#include "nifti1_io.h"
#include "nifti_mex.h"
void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]){
int i;
const char *fnames[42];
int nVols = -1;
int* loadTheseVols = NULL;
int buflen;
char *inFileName;
nifti_image *nim;
mwSize dims[7];
mxClassID dt; mxComplexity cmp = mxREAL;
mxArray *tmp = NULL;
mxArray *dim;
double *dimPtr;
mxArray *pd;
double *pdPtr;
mxArray *qx;
double *qxPtr;
mxArray *qi;
double *qiPtr;
mxArray *sx;
double *sxPtr;
mxArray *si;
double *siPtr;
/* create a Matlab struct for output */
i=0;
fnames[i++] = "data";
fnames[i++] = "fname";
fnames[i++] = "ndim";
fnames[i++] = "dim";
fnames[i++] = "pixdim"; /* voxel size, in xyz_units */
fnames[i++] = "scl_slope";
fnames[i++] = "scl_inter"; /* scaling parameters */
fnames[i++] = "cal_min";
fnames[i++] = "cal_max"; /* calibration parameters */
fnames[i++] = "qform_code";
fnames[i++] = "sform_code"; /* codes for (x,y,z) space meaning */
fnames[i++] = "freq_dim";
fnames[i++] = "phase_dim"; /* indexes (1,2,3, or 0) for MRI */
fnames[i++] = "slice_dim"; /* directions in dim[]/pixdim[] */
fnames[i++] = "slice_code"; /* code for slice timing pattern */
fnames[i++] = "slice_start";
fnames[i++] = "slice_end"; /* indexes for start & stop of slices */
fnames[i++] = "slice_duration";/* time between individual slices */
fnames[i++] = "quatern_b";
fnames[i++] = "quatern_c"; /* quaternion transform parameters */
fnames[i++] = "quatern_d";
fnames[i++] = "qoffset_x"; /* [when writing a dataset, these ] */
fnames[i++] = "qoffset_y";
fnames[i++] = "qoffset_z"; /* [are used for qform, NOT qto_xyz] */
fnames[i++] = "qfac";
fnames[i++] = "qto_xyz"; /* (mat44) qform: transform (i,j,k) to (x,y,z) */
fnames[i++] = "qto_ijk"; /* (mat44) qform: transform (x,y,z) to (i,j,k) */
fnames[i++] = "sto_xyz"; /* (mat44) sform: transform (i,j,k) to (x,y,z) */
fnames[i++] = "sto_ijk"; /* (mat44) sform: transform (x,y,z) to (i,j,k) */
fnames[i++] = "toffset"; /* time coordinate offset */
fnames[i++] = "xyz_units";
fnames[i++] = "time_units"; /* dx,dy,dz & dt units: NIFTI_UNITS_* code */
fnames[i++] = "nifti_type"; /* 0==ANALYZE, 2==NIFTI-1 (2 files), 1==NIFTI-1 (1 file),3==NIFTI-ASCII */
fnames[i++] = "intent_code"; /* statistic type (or something) */
fnames[i++] = "intent_p1";
fnames[i++] = "intent_p2"; /* intent parameters */
fnames[i++] = "intent_p3";
fnames[i++] = "intent_name"; /* char[16] */
fnames[i++] = "descrip"; /* char[80] */
fnames[i++] = "aux_file"; /* char[24] */
fnames[i++] = "num_ext";
plhs[0] = mxCreateStructMatrix(1, 1, i, fnames);
if(nrhs==0&&nlhs==1){
/* In this case, we return an empty nifti struct- Set some simple defaults */
mxSetField(plhs[0], 0, "xyz_units", mxCreateString(getNiftiUnitStrOptions()));
mxSetField(plhs[0], 0, "time_units", mxCreateString(getNiftiUnitStrOptions()));
return;
}
if(nrhs<1||nrhs>2||nlhs>1){
mexPrintf("\nniftiImage = readFileNifti(fileName, [volumesToLoad=-1])\n\n");
mexPrintf("Reads a NIFTI image and populates a structure that should resemble\n");
mexPrintf("the NIFTI 1 standard (see http://nifti.nimh.nih.gov/nifti-1/ ).\n");
mexPrintf("The optional second arg specifies which volumes to load for a 4-d dataset.\n");
mexPrintf("The default (-1) means to read all, [] (empty) will just return the header.\n\n");
mexPrintf("Call this function again with an output argument to get an empty structure.\n\n");
plhs[0] = NULL;
return;
}
/* The first arg must be a string (row-vector char). */
if(mxIsChar(prhs[0])!= 1)
myErrMsg("Input must be a string.");
if(mxGetM(prhs[0])!=1)
myErrMsg("Input must be a row vector.");
/* nVols = -1 means get them all (2nd arg missing or negative) */
if(nrhs>1){
/* The second arg, if present, must be a 1-d array of integers (row-vector int). */
if(!mxIsEmpty(prhs[1]) && !mxIsNumeric(prhs[1]) && mxIsComplex(prhs[1]) && mxGetNumberOfDimensions(prhs[1])>2 && mxGetM(prhs[1])!=1)
myErrMsg("Second input must be a numeric row vector or empty.");
if(mxIsEmpty(prhs[1])){
nVols = 0;
}else{
nVols = mxGetN(prhs[1]);
loadTheseVols = (int *)mxGetPr(prhs[1]);
}
}
/* allocate memory for input string */
buflen = (mxGetM(prhs[0]) * mxGetN(prhs[0])) + 1;
inFileName = (char *)mxCalloc(buflen, sizeof(char));
/* copy the string data from prhs[0] into a C string input_ buf. */
if(mxGetString(prhs[0], inFileName, buflen))
mexWarnMsgTxt("Not enough space. String is truncated.");
/* Load the nifti image */
if(nVols<0){
nim = nifti_image_read(inFileName, 1);
}else if(nVols==0){
nim = nifti_image_read(inFileName, 0);
}else{
/* *** WORK HERE
* We have to change the code below to copy the data from the NB struct
* rather than nim.data, which will be NULL in this case.
*/
myErrMsg("Not yet implemented!");
/*nifti_brick_list NB;
nim = nifti_image_read_bricks("myfile.nii", nVols, loadTheseVols, &NB);*/
}
if(nim == NULL) myErrMsg("nim is NULL! Check to be sure the file exists.");
/*
* Push NIFTI format into a matlab struct.
*/
for(i=0; i<7; i++) dims[i] = nim->dim[i+1];
/* *** TO DO: support all the possible types. */
switch(nim->datatype){
case DT_UINT8: dt=mxUINT8_CLASS; break;
case DT_INT8: dt=mxINT8_CLASS; break;
case DT_UINT16: dt=mxUINT16_CLASS; break;
case DT_INT16: dt=mxINT16_CLASS; break;
case DT_UINT32: dt=mxUINT32_CLASS; break;
case DT_INT32: dt=mxINT32_CLASS; break;
case DT_UINT64: dt=mxUINT64_CLASS; break;
case DT_INT64: dt=mxINT64_CLASS; break;
case DT_FLOAT32: dt=mxSINGLE_CLASS; break;
case DT_FLOAT64: dt=mxDOUBLE_CLASS; break;
case DT_COMPLEX64: dt=mxSINGLE_CLASS; cmp=mxCOMPLEX; break;
case DT_COMPLEX128: dt=mxDOUBLE_CLASS; cmp=mxCOMPLEX; break;
case DT_RGB24: dt=mxUINT8_CLASS; break;
case DT_RGBA32: dt=mxUINT8_CLASS; break;
default: mexErrMsgTxt("Unknown data type!");
}
/*
* Change qto and sto xforms from 0-indexing to 1-indexing.
*/
if(nim->qform_code>0){
nim->qto_ijk.m[0][3] = nim->qto_ijk.m[0][3] + 1;
nim->qto_ijk.m[1][3] = nim->qto_ijk.m[1][3] + 1;
nim->qto_ijk.m[2][3] = nim->qto_ijk.m[2][3] + 1;
nim->qto_xyz = nifti_mat44_inverse(nim->qto_ijk);
nifti_mat44_to_quatern(nim->qto_xyz,
&(nim->quatern_b), &(nim->quatern_c), &(nim->quatern_d),
&(nim->qoffset_x), &(nim->qoffset_y), &(nim->qoffset_z),
&(nim->pixdim[1]), &(nim->pixdim[2]), &(nim->pixdim[3]), &(nim->qfac) ) ;
}
if(nim->sform_code>0){
nim->sto_ijk.m[0][3] = nim->sto_ijk.m[0][3] + 1;
nim->sto_ijk.m[1][3] = nim->sto_ijk.m[1][3] + 1;
nim->sto_ijk.m[2][3] = nim->sto_ijk.m[2][3] + 1;
nim->sto_xyz = nifti_mat44_inverse(nim->sto_ijk);
}
/*
* *** TO DO:
* We copy the NIFTI data to the matlab array. This is much safer
* than trying to pass the nim pointer back, since the nifti routine
* didn't use mxMalloc. It would be more efficient if we could
* allocate the memory block ourselves and tell the nifti lib routine
* to put it there.
*/
if(nVols!=0 && nim->data!=NULL){
tmp = mxCreateNumericArray(nim->ndim, dims, dt, cmp);
/* I assume that we can rely on the nifti routine to byte-swap for us? */
memcpy(mxGetData(tmp), nim->data, nim->nbyper*nim->nvox);
free(nim->data);
mxSetField(plhs[0], 0, "data", tmp);
}
mxSetField(plhs[0], 0, "fname", mxCreateString(nim->fname));
mxSetField(plhs[0], 0, "ndim", mxCreateDoubleScalar(nim->ndim));
dim = mxCreateDoubleMatrix(1,nim->ndim,mxREAL);
dimPtr = (double *)mxGetData(dim);
for(i=0; i<nim->ndim; i++) dimPtr[i] = (double)nim->dim[i+1];
mxSetField(plhs[0], 0, "dim", dim);
/*mxSetField(plhs[0], 0, "datatype", mxCreateDoubleScalar(nim->datatype));*/
pd = mxCreateDoubleMatrix(1,nim->ndim,mxREAL);
pdPtr = (double *)mxGetData(pd);
for(i=0; i<nim->ndim; i++) pdPtr[i] = (double)nim->pixdim[i+1];
mxSetField(plhs[0], 0, "pixdim", pd);
mxSetField(plhs[0], 0, "scl_slope", mxCreateDoubleScalar(nim->scl_slope));
mxSetField(plhs[0], 0, "scl_inter", mxCreateDoubleScalar(nim->scl_inter));
mxSetField(plhs[0], 0, "cal_min", mxCreateDoubleScalar(nim->cal_min));
mxSetField(plhs[0], 0, "cal_max", mxCreateDoubleScalar(nim->cal_max));
mxSetField(plhs[0], 0, "qform_code", mxCreateDoubleScalar(nim->qform_code));
mxSetField(plhs[0], 0, "sform_code", mxCreateDoubleScalar(nim->sform_code));
mxSetField(plhs[0], 0, "freq_dim", mxCreateDoubleScalar(nim->freq_dim));
mxSetField(plhs[0], 0, "phase_dim", mxCreateDoubleScalar(nim->phase_dim));
mxSetField(plhs[0], 0, "slice_dim", mxCreateDoubleScalar(nim->slice_dim));
mxSetField(plhs[0], 0, "slice_code", mxCreateDoubleScalar(nim->slice_code));
mxSetField(plhs[0], 0, "slice_start", mxCreateDoubleScalar(nim->slice_start));
mxSetField(plhs[0], 0, "slice_end", mxCreateDoubleScalar(nim->slice_end));
mxSetField(plhs[0], 0, "slice_duration", mxCreateDoubleScalar(nim->slice_duration));
mxSetField(plhs[0], 0, "quatern_b", mxCreateDoubleScalar(nim->quatern_b));
mxSetField(plhs[0], 0, "quatern_c", mxCreateDoubleScalar(nim->quatern_c));
mxSetField(plhs[0], 0, "quatern_d", mxCreateDoubleScalar(nim->quatern_d));
mxSetField(plhs[0], 0, "qoffset_x", mxCreateDoubleScalar(nim->qoffset_x));
mxSetField(plhs[0], 0, "qoffset_y", mxCreateDoubleScalar(nim->qoffset_y));
mxSetField(plhs[0], 0, "qoffset_z", mxCreateDoubleScalar(nim->qoffset_z));
mxSetField(plhs[0], 0, "qfac", mxCreateDoubleScalar(nim->qfac));
qx = mxCreateDoubleMatrix(4,4,mxREAL);
qxPtr = (double *)mxGetData(qx);
for(i=0; i<16; i++) qxPtr[i] = (double)nim->qto_xyz.m[i%4][i/4];
mxSetField(plhs[0], 0, "qto_xyz", qx);
qi = mxCreateDoubleMatrix(4,4,mxREAL);
qiPtr = (double *)mxGetData(qi);
for(i=0; i<16; i++) qiPtr[i] = (double)nim->qto_ijk.m[i%4][i/4];
mxSetField(plhs[0], 0, "qto_ijk", qi);
sx = mxCreateDoubleMatrix(4,4,mxREAL);
sxPtr = (double *)mxGetData(sx);
for(i=0; i<16; i++) sxPtr[i] = (double)nim->sto_xyz.m[i%4][i/4];
mxSetField(plhs[0], 0, "sto_xyz", sx);
si = mxCreateDoubleMatrix(4,4,mxREAL);
siPtr = (double *)mxGetData(si);
for(i=0; i<16; i++) siPtr[i] = (double)nim->sto_ijk.m[i%4][i/4];
mxSetField(plhs[0], 0, "sto_ijk", si);
mxSetField(plhs[0], 0, "toffset", mxCreateDoubleScalar(nim->toffset));
mxSetField(plhs[0], 0, "xyz_units", mxCreateString(getNiftiUnitStr(nim->xyz_units)));
mxSetField(plhs[0], 0, "time_units", mxCreateString(getNiftiUnitStr(nim->time_units)));
mxSetField(plhs[0], 0, "nifti_type", mxCreateDoubleScalar(nim->nifti_type));
mxSetField(plhs[0], 0, "intent_code", mxCreateDoubleScalar(nim->intent_code));
mxSetField(plhs[0], 0, "intent_p1", mxCreateDoubleScalar(nim->intent_p1));
mxSetField(plhs[0], 0, "intent_p2", mxCreateDoubleScalar(nim->intent_p2));
mxSetField(plhs[0], 0, "intent_p3", mxCreateDoubleScalar(nim->intent_p3));
mxSetField(plhs[0], 0, "intent_name", mxCreateString(nim->intent_name));
mxSetField(plhs[0], 0, "descrip", mxCreateString(nim->descrip));
mxSetField(plhs[0], 0, "aux_file", mxCreateString(nim->aux_file));
mxSetField(plhs[0], 0, "num_ext", mxCreateDoubleScalar(nim->num_ext));
/* *** TO DO: support extended header fileds! */
}
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