c_nifti 0.0.1

data/ext/nifticlib/nifticlib-2.0.0/packaging/DevPackage.template

@@ -0,0 +1,18 @@
+[Setup]
+Version=__major_version__
+AppName=nifticlib
+AppVersion=__full_version__
+AppVerName=nifticlib __full_version__
+MenuName=nifticlib
+Description=Niftilib is a set of i/o libraries for reading and writing files in the NIfTI-1 data format. NIfTI-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images.
+Url=http://niftilib.sourceforge.net/
+License=LICENSE
+Readme=README
+
+[Files]
+bin=<app>\bin\
+include=<app>\include\
+lib=<app>\lib\
+
+[Icons]
+Website=http://niftilib.sourceforge.net

data/ext/nifticlib/nifticlib-2.0.0/packaging/nifticlib.spec

@@ -0,0 +1,62 @@
+Name: nifticlib
+Summary: Niftilib C library
+Version: 1.1.0
+Release: 1
+License: Public Domain
+Group: Applications/Scientific
+Source: %{name}-%{version}.tar.gz
+#Patch1: nifticlib.patch
+URL: http://niftilib.sourceforge.net/
+BuildRoot: %{_tmppath}/%{name}-%{version}-root
+Packager: Andy Loening <loening at alum dot mit dot edu>
+#Requires: openssl
+BuildRequires: cmake
+
+
+%description
+Nifticlib is a set of C i/o libraries for reading and writing files in
+the nifti-1 data format. nifti-1 is a binary file format for storing
+medical image data, e.g. magnetic resonance image (MRI) and functional
+MRI (fMRI) brain images.
+
+%package devel
+Summary: static libraries and header files for nifticlib development
+Group: Development/Libraries
+Requires: nifticlib = %{version}
+
+%description devel
+
+The nifticlib-devel package contains the header files and static libraries
+necessary for developing programs that make use of the nifticlib library.
+
+%prep
+%setup -q
+
+%build
+cmake -DBUILD_SHARED_LIBS=ON -DCMAKE_INSTALL_PREFIX=%{_prefix} -DNIFTI_INSTALL_INCLUDE_DIR=%{_prefix}/include/nifti  .
+make
+
+%install
+rm -rf $RPM_BUILD_ROOT
+make install DESTDIR=$RPM_BUILD_ROOT
+
+## hack to get this to work for x86_64
+%if "%{?_lib}" == "lib64" 
+	mv $RPM_BUILD_ROOT/usr/lib $RPM_BUILD_ROOT/%{_libdir}
+%endif
+
+
+%clean
+rm -rf $RPM_BUILD_ROOT
+
+%files
+%defattr(-,root,root)
+%doc README
+%{_libdir}/*
+#%{_datadir}/doc/*
+
+%files devel
+%defattr(-,root,root)
+%{_bindir}/*
+%{_includedir}/*
+

data/ext/nifticlib/nifticlib-2.0.0/real_easy/nifti1_read_write.c

@@ -0,0 +1,361 @@
+/*********************************************************************
+ *
+ * Very simple code snippets to read/write nifti1 files
+ * This code is placed in the public domain.
+ *
+ * If you are the type who doesn't want to use a file format unless
+ * you can write your own i/o code in less than 30minutes, this
+ * example is for you.
+ *
+ * This code does not deal with wrong-endian data, compressed data,
+ * the new qform/sform orientation codes, parsing filenames, volume-
+ * wise or timecourse-wise data access or any of a million other very useful
+ * things that are in the niftilib i/o reference libraries.
+ * We encourage people to use the niftilib reference library and send
+ * feedback/suggestions, see http://niftilib.sourceforge.net/
+ * But, if that is too much to tackle and you just want to jump in, this
+ * code is a starting point.
+ * This code was written for maximum readability, not for the greatest
+ * coding style.
+ *
+ *
+ * If you are already a little familiar with reading/writing Analyze
+ * files of some flavor, and maybe even have some of your own code, here
+ * are the most important things to be aware of in transitioning to nifti1:
+ *
+ * 1. nii vs .hdr/.img
+ *      nifti1 datasets can be stored either in .hdr/.img pairs of files
+ *      or in 1 .nii file.  In a .nii file the data will start at the byte
+ *      specified by the vox_offset field, which will be 352 if no extensions
+ *      have been added.  And, nifti1 really does like that magic field set
+ *      to "n+1" for .nii and "ni1" for .img/.hdr
+ *
+ * 2. scaling
+ *      nifti1 datasets can contain a scaling factor.  You need to check the
+ *      scl_slope field and if that isn't 0, scale your data by 
+ *      Y * scl_slope  + scl_inter
+ *
+ * 3. extensions
+ *      nifti1 datasets can have some "extension data" stuffed after the 
+ *      regular header.  You can just ignore it, but, be aware that a
+ *      .hdr file may be longer than 348 bytes, and, in a .nii file
+ *      you can't just jump to byte 352, you need to use the vox_offset
+ *      field to get the start of the image data.
+ *
+ * 4. new datatypes
+ *      nifti1 added a few new datatypes that were not in the Analyze 7.5
+ *      format from which nifti1 is derived.  If you're just working with
+ *      your own data this is not an issue but if you get a foreign nifti1
+ *      file, be aware of exotic datatypes like DT_COMPLEX256 and mundane
+ *      things like DT_UINT16.
+ *
+ * 5. other stuff
+ *     nifti1 really does like the dim[0] field set to the number of
+ *     dimensions of the dataset.  Other Analyze flavors might not
+ *     have been so scrupulous about that.
+ *     nifti1 has a bunch of other new fields such as intent codes,
+ *     qform/sform, etc. but, if you just want to get your hands on
+ *     the data blob you can ignore these.  Example use of these fields
+ *     is in the niftilib reference libraries.
+ *
+ *
+ *
+ * To compile:
+ * You need to put a copy of the nifti1.h header file in this directory.
+ * It can be obtained from the NIFTI homepage  http://nifti.nimh.nih.gov/
+ * or from the niftilib SourceForge site http://niftilib.sourceforge.net/
+ * 
+ * cc -o nifti1_read_write nifti1_read_write.c
+ * 
+ * 
+ * To run:
+ * nifti1_read_write -w abc.nii abc.nii
+ * nifti1_read_write -r abc.nii abc.nii
+ * 
+ * 
+ * The read method is hardcoded to read float32 data.  To change
+ * to your datatype, just change the line:
+ * typedef float MY_DATATYPE;
+ *
+ * The write method is hardcoded to write float32 data.  To change
+ * to your datatype, change the line:
+ * typedef float MY_DATATYPE;
+ * and change the lines:
+ * hdr.datatype = NIFTI_TYPE_FLOAT32;
+ * hdr.bitpix = 32;
+ *
+ *
+ * Written by Kate Fissell, University of Pittsburgh, May 2005.
+ *
+ *********************************************************************/
+
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "nifti1.h"
+
+typedef float MY_DATATYPE;
+
+#define MIN_HEADER_SIZE 348
+#define NII_HEADER_SIZE 352
+
+
+main(argc,argv) 
+int argc;
+char *argv[];
+{
+
+char *hdr_file, *data_file;
+short do_read=0;
+short do_write=0;
+
+
+/********** process commandline parameters */
+if (argc != 4) {
+        fprintf(stderr, "\nUsage: %s <-r|-w> <header file> <data file>\n",argv[0]);
+        exit(1);
+}
+
+if (!strncmp(argv[1],"-r",2))
+        do_read=1;
+else if (!strncmp(argv[1],"-w",2))
+        do_write=1;
+else {
+        fprintf(stderr, "\nUsage: %s <-r|-w> <header file> <data file>\n",argv[0]);
+        exit(1);
+}
+
+hdr_file = argv[2];
+data_file = argv[3];
+
+
+
+/********** do the simple read or write */
+if (do_read)
+        read_nifti_file(hdr_file, data_file);
+else if (do_write)
+        write_nifti_file(hdr_file, data_file);
+
+
+exit(0);
+}
+
+/**********************************************************************
+ *
+ * read_nifti_file
+ *
+ **********************************************************************/
+int read_nifti_file(hdr_file, data_file)
+char *hdr_file, *data_file;
+{
+nifti_1_header hdr;
+FILE *fp;
+int ret,i;
+double total;
+MY_DATATYPE *data=NULL;
+
+
+/********** open and read header */
+fp = fopen(hdr_file,"r");
+if (fp == NULL) {
+        fprintf(stderr, "\nError opening header file %s\n",hdr_file);
+        exit(1);
+}
+ret = fread(&hdr, MIN_HEADER_SIZE, 1, fp);
+if (ret != 1) {
+        fprintf(stderr, "\nError reading header file %s\n",hdr_file);
+        exit(1);
+}
+fclose(fp);
+
+
+/********** print a little header information */
+fprintf(stderr, "\n%s header information:",hdr_file);
+fprintf(stderr, "\nXYZT dimensions: %d %d %d %d",hdr.dim[1],hdr.dim[2],hdr.dim[3],hdr.dim[4]);
+fprintf(stderr, "\nDatatype code and bits/pixel: %d %d",hdr.datatype,hdr.bitpix);
+fprintf(stderr, "\nScaling slope and intercept: %.6f %.6f",hdr.scl_slope,hdr.scl_inter);
+fprintf(stderr, "\nByte offset to data in datafile: %ld",(long)(hdr.vox_offset));
+fprintf(stderr, "\n");
+
+
+/********** open the datafile, jump to data offset */
+fp = fopen(data_file,"r");
+if (fp == NULL) {
+        fprintf(stderr, "\nError opening data file %s\n",data_file);
+        exit(1);
+}
+
+ret = fseek(fp, (long)(hdr.vox_offset), SEEK_SET);
+if (ret != 0) {
+        fprintf(stderr, "\nError doing fseek() to %ld in data file %s\n",(long)(hdr.vox_offset), data_file);
+        exit(1);
+}
+
+
+/********** allocate buffer and read first 3D volume from data file */
+data = (MY_DATATYPE *) malloc(sizeof(MY_DATATYPE) * hdr.dim[1]*hdr.dim[2]*hdr.dim[3]);
+if (data == NULL) {
+        fprintf(stderr, "\nError allocating data buffer for %s\n",data_file);
+        exit(1);
+}
+ret = fread(data, sizeof(MY_DATATYPE), hdr.dim[1]*hdr.dim[2]*hdr.dim[3], fp);
+if (ret != hdr.dim[1]*hdr.dim[2]*hdr.dim[3]) {
+        fprintf(stderr, "\nError reading volume 1 from %s (%d)\n",data_file,ret);
+        exit(1);
+}
+fclose(fp);
+
+
+/********** scale the data buffer  */
+if (hdr.scl_slope != 0) {
+        for (i=0; i<hdr.dim[1]*hdr.dim[2]*hdr.dim[3]; i++)
+                data[i] = (data[i] * hdr.scl_slope) + hdr.scl_inter;
+}
+
+
+/********** print mean of data */
+total = 0;
+for (i=0; i<hdr.dim[1]*hdr.dim[2]*hdr.dim[3]; i++)
+        total += data[i];
+total /= (hdr.dim[1]*hdr.dim[2]*hdr.dim[3]);
+fprintf(stderr, "\nMean of volume 1 in %s is %.3f\n",data_file,total);
+
+
+return(0);
+}
+
+
+/**********************************************************************
+ *
+ * write_nifti_file
+ * 
+ * write a sample nifti1 (.nii) data file
+ * datatype is float32
+ * XYZT size is 64x64x16x10
+ * XYZ voxel size is 1mm
+ * TR is 1500ms
+ *
+ **********************************************************************/
+int write_nifti_file(hdr_file, data_file)
+char *hdr_file, *data_file;
+{
+nifti_1_header hdr;
+nifti1_extender pad={0,0,0,0};
+FILE *fp;
+int ret,i;
+MY_DATATYPE *data=NULL;
+short do_nii;
+
+
+/********** make sure user specified .hdr/.img or .nii/.nii */
+if ( (strlen(hdr_file) < 4) || (strlen(data_file) < 4) ) {
+        fprintf(stderr, "\nError: write files must end with .hdr/.img or .nii/.nii extension\n");
+        exit(1);
+}
+
+if ( (!strncmp(hdr_file+(strlen(hdr_file)-4), ".hdr",4)) &&
+     (!strncmp(data_file+(strlen(data_file)-4), ".img",4)) ) {
+        do_nii = 0;
+}
+else if ( (!strncmp(hdr_file+(strlen(hdr_file)-4), ".nii",4)) &&
+     (!strncmp(data_file+(strlen(data_file)-4), ".nii",4)) ) {
+        do_nii = 1;
+}
+else {
+        fprintf(stderr, "\nError: file(s) to be written must end with .hdr/.img or .nii/.nii extension\n");
+        exit(1);
+}
+        
+
+/********** fill in the minimal default header fields */
+bzero((void *)&hdr, sizeof(hdr));
+hdr.sizeof_hdr = MIN_HEADER_SIZE;
+hdr.dim[0] = 4;
+hdr.dim[1] = 64;
+hdr.dim[2] = 64;
+hdr.dim[3] = 16;
+hdr.dim[4] = 10;
+hdr.datatype = NIFTI_TYPE_FLOAT32;
+hdr.bitpix = 32;
+hdr.pixdim[1] = 1.0;
+hdr.pixdim[2] = 1.0;
+hdr.pixdim[3] = 1.0;
+hdr.pixdim[4] = 1.5;
+if (do_nii)
+        hdr.vox_offset = (float) NII_HEADER_SIZE;
+else
+        hdr.vox_offset = (float)0;
+hdr.scl_slope = 100.0;
+hdr.xyzt_units = NIFTI_UNITS_MM | NIFTI_UNITS_SEC;
+if (do_nii)
+        strncpy(hdr.magic, "n+1\0", 4);
+else
+        strncpy(hdr.magic, "ni1\0", 4);
+
+
+/********** allocate buffer and fill with dummy data  */
+data = (MY_DATATYPE *) malloc(sizeof(MY_DATATYPE) * hdr.dim[1]*hdr.dim[2]*hdr.dim[3]*hdr.dim[4]);
+if (data == NULL) {
+        fprintf(stderr, "\nError allocating data buffer for %s\n",data_file);
+        exit(1);
+}
+
+for (i=0; i<hdr.dim[1]*hdr.dim[2]*hdr.dim[3]*hdr.dim[4]; i++)
+        data[i] = i / hdr.scl_slope;
+
+
+/********** write first 348 bytes of header   */
+fp = fopen(hdr_file,"w");
+if (fp == NULL) {
+        fprintf(stderr, "\nError opening header file %s for write\n",hdr_file);
+        exit(1);
+}
+ret = fwrite(&hdr, MIN_HEADER_SIZE, 1, fp);
+if (ret != 1) {
+        fprintf(stderr, "\nError writing header file %s\n",hdr_file);
+        exit(1);
+}
+
+
+/********** if nii, write extender pad and image data   */
+if (do_nii == 1) {
+
+        ret = fwrite(&pad, 4, 1, fp);
+        if (ret != 1) {
+                fprintf(stderr, "\nError writing header file extension pad %s\n",hdr_file);
+                exit(1);
+        }
+
+        ret = fwrite(data, (size_t)(hdr.bitpix/8), hdr.dim[1]*hdr.dim[2]*hdr.dim[3]*hdr.dim[4], fp);
+        if (ret != hdr.dim[1]*hdr.dim[2]*hdr.dim[3]*hdr.dim[4]) {
+                fprintf(stderr, "\nError writing data to %s\n",hdr_file);
+                exit(1);
+        }
+
+        fclose(fp);
+}
+
+
+/********** if hdr/img, close .hdr and write image data to .img */
+else {
+
+        fclose(fp);     /* close .hdr file */
+
+        fp = fopen(data_file,"w");
+        if (fp == NULL) {
+                fprintf(stderr, "\nError opening data file %s for write\n",data_file);
+                exit(1);
+        }
+        ret = fwrite(data, (size_t)(hdr.bitpix/8), hdr.dim[1]*hdr.dim[2]*hdr.dim[3]*hdr.dim[4], fp);
+        if (ret != hdr.dim[1]*hdr.dim[2]*hdr.dim[3]*hdr.dim[4]) {
+                fprintf(stderr, "\nError writing data to %s\n",data_file);
+                exit(1);
+        }
+
+        fclose(fp);
+}
+
+
+
+return(0);
+}

data/ext/nifticlib/nifticlib-2.0.0/utils/CMakeLists.txt

@@ -0,0 +1,73 @@
+#File Generated by Hans J. Johnson
+#Please contact hans-johnson@uiowa.edu for making enhancments/corrections
+PROJECT(NIFTIUTILS)
+
+INCLUDE_DIRECTORIES(${NIFTILIB_SOURCE_DIR} ${ZNZLIB_SOURCE_DIR} ${NIFTICDFLIB_SOURCE_DIR})
+
+ADD_EXECUTABLE(${PACKAGE_PREFIX}nifti_stats nifti_stats.c)
+ADD_EXECUTABLE(${PACKAGE_PREFIX}nifti_tool nifti_tool.c)
+ADD_EXECUTABLE(${PACKAGE_PREFIX}nifti1_test nifti1_test.c)
+TARGET_LINK_LIBRARIES( nifti_stats ${PACKAGE_PREFIX}niftiio ${PACKAGE_PREFIX}nifticdf)
+TARGET_LINK_LIBRARIES( nifti_tool  ${PACKAGE_PREFIX}niftiio)
+TARGET_LINK_LIBRARIES( nifti1_test ${PACKAGE_PREFIX}niftiio)
+
+IF(NOT NIFTI_INSTALL_NO_DEVELOPMENT)
+  INSTALL(TARGETS ${PACKAGE_PREFIX}nifti_stats ${PACKAGE_PREFIX}nifti_tool ${PACKAGE_PREFIX}nifti1_test
+    RUNTIME DESTINATION ${NIFTI_INSTALL_BIN_DIR} COMPONENT RuntimeLibraries
+    LIBRARY DESTINATION ${NIFTI_INSTALL_LIB_DIR} COMPONENT RuntimeLibraries
+    ARCHIVE DESTINATION ${NIFTI_INSTALL_LIB_DIR} COMPONENT Development)
+ENDIF(NOT NIFTI_INSTALL_NO_DEVELOPMENT)
+
+IF(NOT NIFTI_INSTALL_NO_DEVELOPMENT)
+  FILE(GLOB __files "${CMAKE_CURRENT_SOURCE_DIR}/*.h")
+  INSTALL(FILES ${__files}
+    DESTINATION ${NIFTI_INSTALL_INCLUDE_DIR} COMPONENT Development)
+ENDIF(NOT NIFTI_INSTALL_NO_DEVELOPMENT)
+
+ADD_TEST(${PACKAGE_PREFIX}nifti1_test_help ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti1_test)
+ADD_TEST(${PACKAGE_PREFIX}nifti1_test_n1 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti1_test  -n1  ${NIFTI_SOURCE_DIR}/Testing/Data/ATestReferenceImageForReadingAndWriting.nii.gz ${NIFTIUTILS_BINARY_DIR}/n1 )
+ADD_TEST(${PACKAGE_PREFIX}nifti1_test_n2 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti1_test  -n2  ${NIFTI_SOURCE_DIR}/Testing/Data/ATestReferenceImageForReadingAndWriting.nii.gz ${NIFTIUTILS_BINARY_DIR}/n2 )
+ADD_TEST(${PACKAGE_PREFIX}nifti1_test_a2 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti1_test  -a2  ${NIFTI_SOURCE_DIR}/Testing/Data/ATestReferenceImageForReadingAndWriting.nii.gz ${NIFTIUTILS_BINARY_DIR}/a2 )
+ADD_TEST(${PACKAGE_PREFIX}nifti1_test_zn1 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti1_test -zn1 ${NIFTI_SOURCE_DIR}/Testing/Data/ATestReferenceImageForReadingAndWriting.nii.gz ${NIFTIUTILS_BINARY_DIR}/zn1 )
+ADD_TEST(${PACKAGE_PREFIX}nifti1_test_zn2 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti1_test -zn2 ${NIFTI_SOURCE_DIR}/Testing/Data/ATestReferenceImageForReadingAndWriting.nii.gz ${NIFTIUTILS_BINARY_DIR}/zn2 )
+ADD_TEST(${PACKAGE_PREFIX}nifti1_test_za2 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti1_test -za2 ${NIFTI_SOURCE_DIR}/Testing/Data/ATestReferenceImageForReadingAndWriting.nii.gz ${NIFTIUTILS_BINARY_DIR}/za2 )
+
+#The help screens always return 1; ADD_TEST(${PACKAGE_PREFIX}nifti_tool_help ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool)
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_n1 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool  -disp_hdr -infile ${NIFTIUTILS_BINARY_DIR}/n1 )
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_n2 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool  -disp_hdr -infile ${NIFTIUTILS_BINARY_DIR}/n2 )
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_a2 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool  -disp_hdr -infile ${NIFTIUTILS_BINARY_DIR}/a2 )
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_zn1 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -disp_hdr -infile ${NIFTIUTILS_BINARY_DIR}/zn1 )
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_zn2 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -disp_hdr -infile ${NIFTIUTILS_BINARY_DIR}/zn2 )
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_za2 ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -disp_hdr -infile ${NIFTIUTILS_BINARY_DIR}/za2 )
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_diff_hdr ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -diff_hdr -infile ${NIFTIUTILS_BINARY_DIR}/zn1 ${NIFTIUTILS_BINARY_DIR}/zn1 )
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_diff_nims ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -diff_nim -infile ${NIFTIUTILS_BINARY_DIR}/zn1 ${NIFTIUTILS_BINARY_DIR}/zn1 )
+
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_copy_brick_list ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -cbl -prefix cbl_zn1.nii -infile ${NIFTIUTILS_BINARY_DIR}/zn1.nii.gz[0,1])
+#ADD_TEST(${PACKAGE_PREFIX}nifti_tool_copy_collapsed_image /bin/sh ${NIFTI_SOURCE_DIR}/utils/rmthenrun cci_zn1.nii ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -cci 2 2 2 -1 -1 -1 -1 -prefix cci_zn1.nii -infile ${NIFTIUTILS_BINARY_DIR}/zn1.nii.gz )
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_disp_ci ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -disp_ci 2 2 2 -1 0 0 0  -infile ${NIFTIUTILS_BINARY_DIR}/zn1.nii.gz )
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_disp_ts ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -disp_ts 2 2 2 -infile ${NIFTIUTILS_BINARY_DIR}/zn1.nii.gz )
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_strip_extras ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -strip_extras -infile ${NIFTIUTILS_BINARY_DIR}/zn1.nii.gz )
+
+# This test needs a file that has extensions to remove
+#ADD_TEST(${PACKAGE_PREFIX}nifti_tool_rm_ext /bin/sh ${NIFTI_SOURCE_DIR}/utils/rmthenrun rm_ext.nii ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -rm_ext ALL -prefix rm_ext.nii -infile ${NIFTIUTILS_BINARY_DIR}/zn1.nii.gz )
+
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_check_hdr ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -check_hdr -infile ${NIFTIUTILS_BINARY_DIR}/za2 )
+ADD_TEST(${PACKAGE_PREFIX}nifti_tool_check_nim ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_tool -check_nim -infile ${NIFTIUTILS_BINARY_DIR}/za2 )
+
+FOREACH(DISTRIBUTION CORREL TTEST FTEST ZSCORE CHISQ BETA BINOM GAMMA POISSON NORMAL FTEST_NONC CHISQ_NONC LOGISTIC LAPLACE UNIFORM TTEST_NONC WEIBULL CHI INVGAUSS EXTVAL PVAL LOGPVAL LOG10PVAL )
+    ADD_TEST(${PACKAGE_PREFIX}nifti_stats_${DISTRIBUTION}_test ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_stats 0:4:1 ${DISTRIBUTION})
+    ADD_TEST(q${PACKAGE_PREFIX}nifti_stats_${DISTRIBUTION}_test ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_stats -q 0:4:1 ${DISTRIBUTION})
+    ADD_TEST(q1${PACKAGE_PREFIX}nifti_stats_${DISTRIBUTION}_test ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_stats -q 0:4:1 ${DISTRIBUTION} 1 1 1)
+    ADD_TEST(d${PACKAGE_PREFIX}nifti_stats_${DISTRIBUTION}_test ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_stats -d 0:4:1 ${DISTRIBUTION})
+    ADD_TEST(d1${PACKAGE_PREFIX}nifti_stats_${DISTRIBUTION}_test ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_stats -d 0:4:1 ${DISTRIBUTION} 1 1 1)
+    ADD_TEST(1${PACKAGE_PREFIX}nifti_stats_${DISTRIBUTION}_test ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_stats -1 0:4:1 ${DISTRIBUTION})
+    ADD_TEST(11${PACKAGE_PREFIX}nifti_stats_${DISTRIBUTION}_test ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_stats -1 0:4:1 ${DISTRIBUTION} 1 1 1)
+    ADD_TEST(z${PACKAGE_PREFIX}nifti_stats_${DISTRIBUTION}_test ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_stats -z 0:4:1 ${DISTRIBUTION})
+    ADD_TEST(z1${PACKAGE_PREFIX}nifti_stats_${DISTRIBUTION}_test ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_stats -z 0:4:1 ${DISTRIBUTION} 1 1 1)
+    ADD_TEST(h${PACKAGE_PREFIX}nifti_stats_${DISTRIBUTION}_test ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_stats -h 0:4:1 ${DISTRIBUTION})
+    ADD_TEST(h1${PACKAGE_PREFIX}nifti_stats_${DISTRIBUTION}_test ${NIFTIUTILS_BINARY_DIR}/${PACKAGE_PREFIX}nifti_stats -h 0:4:1 ${DISTRIBUTION} 1 1 1)
+ENDFOREACH(DISTRIBUTION)
+
+
+
+