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nifticlib-docs-2.0.0-2.fc14.x86_64.rpm

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<div class="title">/builddir/build/BUILD/nifticlib-2.0.0/fsliolib/fslio.h</div>  </div>
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<div class="contents">
<a href="fslio_8h.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 
<a name="l00005"></a>00005 <span class="comment">/*</span>
<a name="l00006"></a>00006 <span class="comment">    fslio.h  (Input and output routines for images in FSL)</span>
<a name="l00007"></a>00007 <span class="comment"></span>
<a name="l00008"></a>00008 <span class="comment">    Mark Jenkinson</span>
<a name="l00009"></a>00009 <span class="comment">    FMRIB Image Analysis Group</span>
<a name="l00010"></a>00010 <span class="comment"></span>
<a name="l00011"></a>00011 <span class="comment">*/</span>
<a name="l00012"></a>00012 
<a name="l00013"></a>00013     
<a name="l00014"></a>00014 <span class="comment">/*</span>
<a name="l00015"></a>00015 <span class="comment">    The fslio.h file was originally part of FSL - FMRIB&#39;s Software Library</span>
<a name="l00016"></a>00016 <span class="comment">    http://www.fmrib.ox.ac.uk/fsl</span>
<a name="l00017"></a>00017 <span class="comment">    fslio.h has now been placed in the public domain.</span>
<a name="l00018"></a>00018 <span class="comment">   </span>
<a name="l00019"></a>00019 <span class="comment">    Developed at FMRIB (Oxford Centre for Functional Magnetic Resonance</span>
<a name="l00020"></a>00020 <span class="comment">    Imaging of the Brain), Department of Clinical Neurology, Oxford</span>
<a name="l00021"></a>00021 <span class="comment">    University, Oxford, UK</span>
<a name="l00022"></a>00022 <span class="comment">*/</span>
<a name="l00023"></a>00023 
<a name="l00024"></a>00024 <span class="preprocessor">#if !defined(__FSLIO_H)</span>
<a name="l00025"></a>00025 <span class="preprocessor"></span><span class="preprocessor">#define __FSLIO_H</span>
<a name="l00026"></a>00026 <span class="preprocessor"></span>
<a name="l00027"></a>00027 <span class="preprocessor">#include &lt;stdio.h&gt;</span>
<a name="l00028"></a>00028 <span class="preprocessor">#include &lt;<a class="code" href="nifti1__io_8h.html" title="Data structures for using nifti1_io API.">nifti1_io.h</a>&gt;</span>
<a name="l00029"></a>00029 <span class="preprocessor">#include &lt;znzlib.h&gt;</span>
<a name="l00030"></a>00030 <span class="preprocessor">#include &quot;dbh.h&quot;</span>
<a name="l00031"></a>00031 
<a name="l00032"></a>00032 <span class="preprocessor">#ifdef __cplusplus</span>
<a name="l00033"></a>00033 <span class="preprocessor"></span><span class="keyword">extern</span> <span class="stringliteral">&quot;C&quot;</span> {
<a name="l00034"></a>00034 <span class="preprocessor">#endif</span>
<a name="l00035"></a>00035 <span class="preprocessor"></span>
<a name="l00036"></a>00036 
<a name="l00037"></a>00037   <span class="comment">/*</span>
<a name="l00038"></a>00038 <span class="comment">    Note that this library is similar to avwio but has changed in many ways.</span>
<a name="l00039"></a>00039 <span class="comment">    It is almost fully backwards compatible, but not quite, as it cannot write</span>
<a name="l00040"></a>00040 <span class="comment">    .nii.gz files using the old style functions.</span>
<a name="l00041"></a>00041 <span class="comment"></span>
<a name="l00042"></a>00042 <span class="comment">    Recommended ways of reading and writing images are:</span>
<a name="l00043"></a>00043 <span class="comment"></span>
<a name="l00044"></a>00044 <span class="comment">    Reading</span>
<a name="l00045"></a>00045 <span class="comment">    -------</span>
<a name="l00046"></a>00046 <span class="comment">      Use the FslOpen(), FslReadVolumes() and FslClose() functions.  e.g.</span>
<a name="l00047"></a>00047 <span class="comment">        FSLIO *fslio;</span>
<a name="l00048"></a>00048 <span class="comment">        void *buffer;</span>
<a name="l00049"></a>00049 <span class="comment">        int nvols;</span>
<a name="l00050"></a>00050 <span class="comment">        fslio = FslOpen(&quot;/some/path/name_of_file&quot;,&quot;rb&quot;);</span>
<a name="l00051"></a>00051 <span class="comment">          ... can now access header info via the FslGet calls ...</span>
<a name="l00052"></a>00052 <span class="comment">          ... allocate room for buffer ...</span>
<a name="l00053"></a>00053 <span class="comment">        FslReadVolumes(fslio,buffer,nvols);</span>
<a name="l00054"></a>00054 <span class="comment">          ... do something ...</span>
<a name="l00055"></a>00055 <span class="comment">        FslClose(fslio);</span>
<a name="l00056"></a>00056 <span class="comment"></span>
<a name="l00057"></a>00057 <span class="comment"></span>
<a name="l00058"></a>00058 <span class="comment">    Writing</span>
<a name="l00059"></a>00059 <span class="comment">    -------</span>
<a name="l00060"></a>00060 <span class="comment">      This is more complicated due to the nature of gzipped writing, which must be</span>
<a name="l00061"></a>00061 <span class="comment">      done in the correct order, and for single files (*.nii.gz) this means that </span>
<a name="l00062"></a>00062 <span class="comment">      the header information must be written before any image data.</span>
<a name="l00063"></a>00063 <span class="comment"></span>
<a name="l00064"></a>00064 <span class="comment">    (1)</span>
<a name="l00065"></a>00065 <span class="comment">      The best method to use is almost backwards compatible, but requires </span>
<a name="l00066"></a>00066 <span class="comment">      an FslWriteHeader() call:</span>
<a name="l00067"></a>00067 <span class="comment"></span>
<a name="l00068"></a>00068 <span class="comment">        FSLIO* fslio;</span>
<a name="l00069"></a>00069 <span class="comment">        fslio = FslOpen(&quot;/some/path/name_of_file&quot;,&quot;wb&quot;);</span>
<a name="l00070"></a>00070 <span class="comment">          ... set the appropriate header information using FslSet calls ...</span>
<a name="l00071"></a>00071 <span class="comment">        FslWriteHeader(fslio);</span>
<a name="l00072"></a>00072 <span class="comment">        </span>
<a name="l00073"></a>00073 <span class="comment">          ... now can write one or more volumes at a time using </span>
<a name="l00074"></a>00074 <span class="comment">              FslWriteVolumes(fslio,buffer,nvols) ...</span>
<a name="l00075"></a>00075 <span class="comment"></span>
<a name="l00076"></a>00076 <span class="comment">        FslClose(fslio); </span>
<a name="l00077"></a>00077 <span class="comment"></span>
<a name="l00078"></a>00078 <span class="comment">      This version is useful if your image data needs to be written from different blocks</span>
<a name="l00079"></a>00079 <span class="comment">      of memory.</span>
<a name="l00080"></a>00080 <span class="comment"></span>
<a name="l00081"></a>00081 <span class="comment">    (2)</span>
<a name="l00082"></a>00082 <span class="comment">      Another method is available, but which is discouraged, is:</span>
<a name="l00083"></a>00083 <span class="comment">        FSLIO* fslio;</span>
<a name="l00084"></a>00084 <span class="comment">        fslio = FslOpen(&quot;/some/path/name_of_file&quot;,&quot;wb&quot;);</span>
<a name="l00085"></a>00085 <span class="comment">        </span>
<a name="l00086"></a>00086 <span class="comment">          ... set some appropriate header information using FslSet calls ...</span>
<a name="l00087"></a>00087 <span class="comment">          ... now can write one or more volumes at a time using </span>
<a name="l00088"></a>00088 <span class="comment">              FslWriteVolumes(fslio,buffer,nvols) ...</span>
<a name="l00089"></a>00089 <span class="comment">          ... set more appropriate header information using FslSet calls ...</span>
<a name="l00090"></a>00090 <span class="comment"></span>
<a name="l00091"></a>00091 <span class="comment">        FslClose(fslio);</span>
<a name="l00092"></a>00092 <span class="comment"></span>
<a name="l00093"></a>00093 <span class="comment">      WARNING: this cannot write .nii.gz files as the header information cannot be</span>
<a name="l00094"></a>00094 <span class="comment">      written by FslClose() after the image data is written, which is how the previous</span>
<a name="l00095"></a>00095 <span class="comment">      versions have worked.</span>
<a name="l00096"></a>00096 <span class="comment">        </span>
<a name="l00097"></a>00097 <span class="comment"></span>
<a name="l00098"></a>00098 <span class="comment">   */</span>
<a name="l00099"></a>00099 
<a name="l00104"></a>00104 <span class="preprocessor">#define FSL_TYPE_ANALYZE         0</span>
<a name="l00105"></a>00105 <span class="preprocessor"></span><span class="preprocessor">#define FSL_TYPE_NIFTI           1</span>
<a name="l00106"></a>00106 <span class="preprocessor"></span><span class="preprocessor">#define FSL_TYPE_NIFTI_PAIR      2</span>
<a name="l00107"></a>00107 <span class="preprocessor"></span><span class="preprocessor">#define FSL_TYPE_MINC            4</span>
<a name="l00108"></a>00108 <span class="preprocessor"></span><span class="preprocessor">#define FSL_TYPE_ANALYZE_GZ    100</span>
<a name="l00109"></a>00109 <span class="preprocessor"></span><span class="preprocessor">#define FSL_TYPE_NIFTI_GZ      101</span>
<a name="l00110"></a>00110 <span class="preprocessor"></span><span class="preprocessor">#define FSL_TYPE_NIFTI_PAIR_GZ 102</span>
<a name="l00111"></a>00111 <span class="preprocessor"></span><span class="preprocessor">#define FSL_TYPE_MINC_GZ       104</span>
<a name="l00112"></a>00112 <span class="preprocessor"></span><span class="comment">/* @} */</span>
<a name="l00113"></a>00113 
<a name="l00114"></a>00114 <span class="preprocessor">#define FSL_RADIOLOGICAL        -1</span>
<a name="l00115"></a>00115 <span class="preprocessor"></span><span class="preprocessor">#define FSL_NEUROLOGICAL         1</span>
<a name="l00116"></a>00116 <span class="preprocessor"></span>
<a name="l00117"></a>00117 
<a name="l00123"></a><a class="code" href="structFSLIO.html">00123</a> <span class="keyword">typedef</span> <span class="keyword">struct </span>
<a name="l00124"></a>00124 {
<a name="l00125"></a>00125   <a class="code" href="structznzptr.html">znzFile</a> fileptr;
<a name="l00126"></a>00126   <a class="code" href="structnifti__image.html" title="High level data structure for open nifti datasets in the nifti1_io API. Note that this structure is n...">nifti_image</a> *niftiptr;
<a name="l00127"></a>00127 <span class="preprocessor">#ifdef USE_MINC</span>
<a name="l00128"></a>00128 <span class="preprocessor"></span>  minc_image *mincptr;
<a name="l00129"></a>00129 <span class="preprocessor">#else</span>
<a name="l00130"></a>00130 <span class="preprocessor"></span>  <span class="keywordtype">void</span> *mincptr;
<a name="l00131"></a>00131 <span class="preprocessor">#endif</span>
<a name="l00132"></a>00132 <span class="preprocessor"></span>  <span class="keywordtype">int</span> file_mode;
<a name="l00133"></a>00133   <span class="keywordtype">int</span> write_mode;
<a name="l00134"></a>00134   <span class="keywordtype">int</span> written_hdr;
<a name="l00135"></a>00135 } <a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a>;
<a name="l00136"></a>00136 
<a name="l00137"></a>00137 
<a name="l00138"></a>00138   <span class="comment">/* basic file i/o commands */</span>
<a name="l00139"></a>00139 
<a name="l00140"></a>00140 <a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *<a class="code" href="fslio_8c.html#ad042b69dce4d4b6a0e6d48e5519e8941" title="Opens a file for either reading or writing.">FslOpen</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *filename, <span class="keyword">const</span> <span class="keywordtype">char</span> *opts);
<a name="l00141"></a>00141 <a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *<a class="code" href="fslio_8c.html#aeda7dfaf2b35bb9b6985cc0fefe389c8" title="Opens a file for either reading or writing.">FslXOpen</a>(<span class="keyword">const</span> <span class="keywordtype">char</span> *filename, <span class="keyword">const</span> <span class="keywordtype">char</span> *opts, <span class="keywordtype">int</span> filetype);
<a name="l00142"></a>00142 <span class="keywordtype">int</span> FslSeekVolume(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">size_t</span> vols);
<a name="l00143"></a>00143 <span class="keywordtype">int</span> <a class="code" href="fslio_8c.html#a417d6fbf3035e9d028a4e3dafa7a7f18" title="Write header and image data if this dataset was open for writing. Close the dataset header and data f...">FslClose</a>(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio);
<a name="l00144"></a>00144 
<a name="l00145"></a>00145   <span class="comment">/* basic read and write commands */</span>
<a name="l00146"></a>00146 
<a name="l00147"></a>00147 <span class="keywordtype">void</span>* <a class="code" href="fslio_8c.html#aee57f4c5d77fad8382354ee3c6ab9895" title="Read the header and all data into the FSLIO structure.">FslReadAllVolumes</a>(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a>* fslio, <span class="keywordtype">char</span>* filename);
<a name="l00148"></a>00148 <span class="keywordtype">void</span>  <a class="code" href="fslio_8c.html#aa7b3ec44398ccdec59cd42e026e57dd3" title="Writes all data from buffer (using size info from fslio) to file.">FslWriteAllVolumes</a>(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keyword">const</span> <span class="keywordtype">void</span> *buffer);
<a name="l00149"></a>00149 
<a name="l00150"></a>00150 <span class="keywordtype">size_t</span> <a class="code" href="fslio_8c.html#aec173c9ecb7af93bea8365dd37cc9901" title="Read the first nvols Volumes from a 4D dataset.">FslReadVolumes</a>(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">void</span> *buffer, <span class="keywordtype">size_t</span> nvols);
<a name="l00151"></a>00151 <span class="keywordtype">size_t</span> <a class="code" href="fslio_8c.html#af49ad010bf6d549a64952a8c1314e0d5" title="Write the first nvols volumes in buffer to disk.">FslWriteVolumes</a>(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keyword">const</span> <span class="keywordtype">void</span> *buffer, <span class="keywordtype">size_t</span> nvols);
<a name="l00152"></a>00152 
<a name="l00153"></a>00153 <span class="keywordtype">void</span>   <a class="code" href="fslio_8c.html#a97f42cbeda1175ea20456d3de7802964" title="Writes nifti/anz header and opens img file ready for writing.">FslWriteHeader</a>(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio);
<a name="l00154"></a>00154 
<a name="l00155"></a>00155   <span class="comment">/* support functions for file names and types */</span>
<a name="l00156"></a>00156 
<a name="l00157"></a>00157 <span class="keywordtype">int</span>   FslFileExists(<span class="keyword">const</span> <span class="keywordtype">char</span> *filename);
<a name="l00158"></a>00158 <span class="keywordtype">char</span> *FslMakeBaseName(<span class="keyword">const</span> <span class="keywordtype">char</span> *fname);
<a name="l00159"></a>00159 <span class="keywordtype">int</span>   FslCheckForMultipleFileNames(<span class="keyword">const</span> <span class="keywordtype">char</span>* filename);
<a name="l00160"></a>00160 <span class="keywordtype">int</span>   FslGetEnvOutputType(<span class="keywordtype">void</span>);
<a name="l00161"></a>00161 
<a name="l00162"></a>00162 <span class="keywordtype">void</span>  FslSetIgnoreMFQ(<span class="keywordtype">int</span> flag);
<a name="l00163"></a>00163 <span class="keywordtype">int</span>   FslGetIgnoreMFQ(<span class="keywordtype">void</span>);
<a name="l00164"></a>00164 <span class="keywordtype">void</span>  FslSetOverrideOutputType(<span class="keywordtype">int</span> type);
<a name="l00165"></a>00165 <span class="keywordtype">int</span>   FslGetOverrideOutputType(<span class="keywordtype">void</span>);
<a name="l00166"></a>00166 
<a name="l00167"></a>00167 
<a name="l00168"></a>00168 <span class="keywordtype">int</span>  FslGetFileType(<span class="keyword">const</span> <a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio);
<a name="l00169"></a>00169 <span class="keywordtype">void</span> FslSetFileType(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">int</span> filetype);
<a name="l00170"></a>00170 <span class="keywordtype">int</span>  FslIsSingleFileType(<span class="keywordtype">int</span> filetype);
<a name="l00171"></a>00171 <span class="keywordtype">int</span>  FslIsCompressedFileType(<span class="keywordtype">int</span> filetype);
<a name="l00172"></a>00172 <span class="keywordtype">int</span>  FslBaseFileType(<span class="keywordtype">int</span> filetype);
<a name="l00173"></a>00173 <span class="keywordtype">char</span>* <a class="code" href="fslio_8c.html#a93be59788d28786380c85b0a0f57b397" title="Return a string describing the format of the dataset.">FslFileTypeString</a>(<span class="keywordtype">int</span> filetype);
<a name="l00174"></a>00174 
<a name="l00175"></a>00175 <span class="keywordtype">int</span>  FslGetWriteMode(<span class="keyword">const</span> <a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio);
<a name="l00176"></a>00176 <span class="keywordtype">void</span> FslSetWriteMode(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">int</span> mode);
<a name="l00177"></a>00177 
<a name="l00178"></a>00178 <span class="keywordtype">void</span> AvwSwapHeader(<span class="keyword">struct</span> <a class="code" href="structdsr.html">dsr</a> *avw);
<a name="l00179"></a>00179 <span class="keywordtype">int</span>  FslReadRawHeader(<span class="keywordtype">void</span> *buffer, <span class="keyword">const</span> <span class="keywordtype">char</span>* filename);
<a name="l00180"></a>00180 
<a name="l00181"></a>00181 
<a name="l00182"></a>00182   <span class="comment">/* simple creation and clone/copy operations */</span>
<a name="l00183"></a>00183 
<a name="l00184"></a>00184 <a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *<a class="code" href="fslio_8c.html#acc3ed701d5eff4e5c2f7fb829e754396" title="allocate space for the FSLIO struct and set some sensible defaults">FslInit</a>(<span class="keywordtype">void</span>);
<a name="l00185"></a>00185 <span class="keywordtype">void</span>   FslInitHeader(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">short</span> t, 
<a name="l00186"></a>00186                    <span class="keywordtype">size_t</span> x, <span class="keywordtype">size_t</span> y, <span class="keywordtype">size_t</span> z, <span class="keywordtype">size_t</span> v,
<a name="l00187"></a>00187                    <span class="keywordtype">float</span> vx, <span class="keywordtype">float</span> vy, <span class="keywordtype">float</span> vz, <span class="keywordtype">float</span> tr,
<a name="l00188"></a>00188                    <span class="keywordtype">size_t</span> dim,
<a name="l00189"></a>00189                    <span class="keyword">const</span> <span class="keywordtype">char</span>* units);
<a name="l00190"></a>00190 <span class="keywordtype">void</span>   FslSetInit(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a>* fslio);
<a name="l00191"></a>00191 <span class="keywordtype">void</span>   FslCloneHeader(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *dest, <span class="keyword">const</span> <a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *src);
<a name="l00192"></a>00192 
<a name="l00193"></a>00193 
<a name="l00194"></a>00194   <span class="comment">/* get and set routines for properties */</span>
<a name="l00195"></a>00195 
<a name="l00196"></a>00196 <span class="keywordtype">size_t</span> FslGetVolSize(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio);
<a name="l00197"></a>00197 
<a name="l00198"></a>00198 <span class="keywordtype">void</span> FslSetDim(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">short</span> x, <span class="keywordtype">short</span> y, <span class="keywordtype">short</span> z, <span class="keywordtype">short</span> v);
<a name="l00199"></a>00199 <span class="keywordtype">void</span> FslGetDim(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">short</span> *x, <span class="keywordtype">short</span> *y, <span class="keywordtype">short</span> *z, <span class="keywordtype">short</span> *v);
<a name="l00200"></a>00200 <span class="keywordtype">void</span> FslSetDimensionality(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">size_t</span> dim);
<a name="l00201"></a>00201 <span class="keywordtype">void</span> FslGetDimensionality(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">size_t</span> *dim);
<a name="l00202"></a>00202 <span class="keywordtype">void</span> FslSetVoxDim(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">float</span> x, <span class="keywordtype">float</span> y, <span class="keywordtype">float</span> z, <span class="keywordtype">float</span> tr);
<a name="l00203"></a>00203 <span class="keywordtype">void</span> FslGetVoxDim(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">float</span> *x, <span class="keywordtype">float</span> *y, <span class="keywordtype">float</span> *z, <span class="keywordtype">float</span> *tr);
<a name="l00204"></a>00204 <span class="keywordtype">void</span> FslGetCalMinMax(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">float</span> *min, <span class="keywordtype">float</span> *max);
<a name="l00205"></a>00205 <span class="keywordtype">void</span> FslSetCalMinMax(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">float</span>  min, <span class="keywordtype">float</span>  max);
<a name="l00206"></a>00206 <span class="keywordtype">void</span> FslGetAuxFile(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio,<span class="keywordtype">char</span> *aux_file);
<a name="l00207"></a>00207 <span class="keywordtype">void</span> FslSetAuxFile(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio,<span class="keyword">const</span> <span class="keywordtype">char</span> *aux_file);
<a name="l00208"></a>00208 <span class="keywordtype">void</span> FslSetTimeUnits(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keyword">const</span> <span class="keywordtype">char</span> *units);
<a name="l00209"></a>00209 <span class="keywordtype">void</span> FslGetTimeUnits(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">char</span> *units);
<a name="l00210"></a>00210 <span class="keywordtype">void</span> FslSetDataType(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">short</span> t);
<a name="l00211"></a>00211 <span class="keywordtype">size_t</span> FslGetDataType(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">short</span> *t);
<a name="l00212"></a>00212 <span class="keywordtype">int</span>    FslGetIntensityScaling(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">float</span> *slope, <span class="keywordtype">float</span> *intercept);
<a name="l00213"></a>00213 <span class="keywordtype">void</span>   FslSetIntent(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">short</span> intent_code, <span class="keywordtype">float</span> p1, <span class="keywordtype">float</span> p2, <span class="keywordtype">float</span> p3);
<a name="l00214"></a>00214 <span class="keywordtype">short</span>  FslGetIntent(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">short</span> *intent_code, <span class="keywordtype">float</span> *p1, <span class="keywordtype">float</span> *p2,
<a name="l00215"></a>00215                     <span class="keywordtype">float</span> *p3);
<a name="l00216"></a>00216 
<a name="l00217"></a>00217 
<a name="l00218"></a>00218 <span class="keywordtype">short</span> FslGetStdXform(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <a class="code" href="structmat44.html">mat44</a> *stdmat);
<a name="l00219"></a>00219 <span class="keywordtype">void</span>  FslSetStdXform(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">short</span> sform_code, <a class="code" href="structmat44.html">mat44</a> stdmat);
<a name="l00220"></a>00220 <span class="keywordtype">void</span>  FslGetMMCoord(<a class="code" href="structmat44.html">mat44</a> stdmat, <span class="keywordtype">float</span> voxx, <span class="keywordtype">float</span> voxy, <span class="keywordtype">float</span> voxz, 
<a name="l00221"></a>00221                     <span class="keywordtype">float</span> *mmx, <span class="keywordtype">float</span> *mmy, <span class="keywordtype">float</span> *mmz);
<a name="l00222"></a>00222 
<a name="l00223"></a>00223 <span class="keywordtype">void</span>  FslGetVoxCoord(<a class="code" href="structmat44.html">mat44</a> stdmat, <span class="keywordtype">float</span> mmx, <span class="keywordtype">float</span> mmy, <span class="keywordtype">float</span> mmz, 
<a name="l00224"></a>00224                      <span class="keywordtype">float</span> *voxx, <span class="keywordtype">float</span> *voxy, <span class="keywordtype">float</span> *voxz); 
<a name="l00225"></a>00225 <span class="keywordtype">short</span> FslGetRigidXform(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <a class="code" href="structmat44.html">mat44</a> *rigidmat);
<a name="l00226"></a>00226 <span class="keywordtype">void</span>  FslSetRigidXform(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">short</span> qform_code, <a class="code" href="structmat44.html">mat44</a> rigidmat);
<a name="l00227"></a>00227 <span class="keywordtype">int</span>   FslGetLeftRightOrder(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio);
<a name="l00228"></a>00228 
<a name="l00229"></a>00229   <span class="comment">/* these two functions are deprecated with the nifti/analyze support */</span>
<a name="l00230"></a>00230   <span class="comment">/* please do all spatial coordinate origins via the Std and Rigid Xforms */</span>
<a name="l00231"></a>00231 <span class="keywordtype">void</span>  FslSetAnalyzeSform(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keyword">const</span> <span class="keywordtype">short</span> *orig, 
<a name="l00232"></a>00232                          <span class="keywordtype">float</span> dx, <span class="keywordtype">float</span> dy, <span class="keywordtype">float</span> dz);
<a name="l00233"></a>00233 <span class="keywordtype">void</span>  FslGetAnalyzeOrigin(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">short</span> orig[5]);
<a name="l00234"></a>00234 
<a name="l00235"></a>00235   <span class="comment">/* other read and write commands */</span>
<a name="l00236"></a>00236 
<a name="l00237"></a>00237 <span class="keywordtype">size_t</span> <a class="code" href="fslio_8c.html#ab2fcd2b0ccb4f917552adb27a28245ee" title="Read one slice from each of the first nvols volumes in the dataset, ie get an xyt buffer...">FslReadSliceSeries</a>(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">void</span> *buffer,<span class="keywordtype">short</span> slice, <span class="keywordtype">size_t</span> nvols);
<a name="l00238"></a>00238 <span class="keywordtype">size_t</span> <a class="code" href="fslio_8c.html#aabc65d9d33f78cad78438a8fe30f2047" title="Read one row from one slice for first nvols volumes in dataset; ie get an xt buffer.">FslReadRowSeries</a>(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">void</span> *buffer, <span class="keywordtype">short</span> row, <span class="keywordtype">short</span> slice, <span class="keywordtype">size_t</span> nvols);
<a name="l00239"></a>00239 <span class="keywordtype">size_t</span> <a class="code" href="fslio_8c.html#a9bf6475860f2a1f4baa5b2cd43ac08a0" title="Read one voxel (xyz location) from first nvols volumes in dataset; ie get a t dim buffer...">FslReadTimeSeries</a>(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">void</span> *buffer, <span class="keywordtype">short</span> xVox, <span class="keywordtype">short</span> yVox, <span class="keywordtype">short</span> zVox, <span class="keywordtype">size_t</span> nvols);
<a name="l00240"></a>00240 
<a name="l00241"></a>00241   <span class="comment">/* miscellaneous helper stuff */</span>
<a name="l00242"></a>00242 
<a name="l00243"></a>00243 <a class="code" href="structmat33.html">mat33</a> mat44_to_mat33(<a class="code" href="structmat44.html">mat44</a> x);
<a name="l00244"></a>00244 
<a name="l00245"></a>00245 
<a name="l00246"></a>00246 
<a name="l00247"></a>00247 <span class="comment">/* added by KF pending discussion w/ Mark */</span>
<a name="l00248"></a>00248 <span class="keyword">typedef</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">char</span>   THIS_UINT8; 
<a name="l00249"></a>00249 <span class="keyword">typedef</span> <span class="keywordtype">char</span>            THIS_INT8;
<a name="l00250"></a>00250 <span class="keyword">typedef</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">short</span>  THIS_UINT16;
<a name="l00251"></a>00251 <span class="keyword">typedef</span> <span class="keywordtype">short</span>           THIS_INT16;
<a name="l00252"></a>00252 <span class="keyword">typedef</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">int</span>    THIS_UINT32;
<a name="l00253"></a>00253 <span class="keyword">typedef</span> <span class="keywordtype">int</span>             THIS_INT32;
<a name="l00254"></a>00254 <span class="keyword">typedef</span> <span class="keywordtype">unsigned</span> <span class="keywordtype">long</span>   THIS_UINT64;
<a name="l00255"></a>00255 <span class="keyword">typedef</span> <span class="keywordtype">long</span>            THIS_INT64;
<a name="l00256"></a>00256 <span class="keyword">typedef</span> <span class="keywordtype">float</span>           THIS_FLOAT32;
<a name="l00257"></a>00257 <span class="keyword">typedef</span> <span class="keywordtype">double</span>          THIS_FLOAT64;
<a name="l00258"></a>00258 
<a name="l00259"></a>00259 <a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> * <a class="code" href="fslio_8c.html#aa745e53a297eb7ffdabfdd89eb1965d6" title="Reads nifti/anz header, no data is read.">FslReadHeader</a>(<span class="keywordtype">char</span> *fname);
<a name="l00260"></a>00260 <span class="keywordtype">double</span> ****<a class="code" href="fslio_8c.html#a8f4c12a7a66d6b19ba9cdea23fd2a1ea" title="Return the fslio data buffer of a 1-4D dataset as a 4D array of scaled doubles.">FslGetBufferAsScaledDouble</a>(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio);
<a name="l00261"></a>00261 <span class="keywordtype">double</span> ***<a class="code" href="fslio_8c.html#a9e2228ced70078b0229bb25e5db7d264" title="Return volume #vol (0-based) as a 3D array of scaled doubles.">FslGetVolumeAsScaledDouble</a>(<a class="code" href="structFSLIO.html" title="High level data structure for open datasets in the fslio API.">FSLIO</a> *fslio, <span class="keywordtype">int</span> vol);
<a name="l00262"></a>00262 <span class="keywordtype">int</span>  <a class="code" href="fslio_8c.html#ab49bea537966913a5c87768a8a073a40" title="allocate a 4D buffer, use 1 contiguous buffer for the data">convertBufferToScaledDouble</a>(<span class="keywordtype">double</span> *outbuf, <span class="keywordtype">void</span> *inbuf, <span class="keywordtype">long</span> len, <span class="keywordtype">float</span> slope, <span class="keywordtype">float</span> inter, <span class="keywordtype">int</span> nifti_datatype ) ;
<a name="l00263"></a>00263 <span class="keywordtype">double</span> ****<a class="code" href="fslio_8c.html#ae129105a692aad358009aa62c0309285" title="allocate a 4D buffer, use 1 contiguous buffer for the data">d4matrix</a>(<span class="keywordtype">int</span> th, <span class="keywordtype">int</span> zh,  <span class="keywordtype">int</span> yh, <span class="keywordtype">int</span> xh);
<a name="l00264"></a>00264 <span class="keywordtype">double</span> ***<a class="code" href="fslio_8c.html#aaea8a976fbe1f9bee250eb8aec155606" title="allocate a 3D buffer, use 1 contiguous buffer for the data">d3matrix</a>(<span class="keywordtype">int</span> zh,  <span class="keywordtype">int</span> yh, <span class="keywordtype">int</span> xh);
<a name="l00265"></a>00265 
<a name="l00266"></a>00266 
<a name="l00267"></a>00267 <span class="preprocessor">#ifdef __cplusplus</span>
<a name="l00268"></a>00268 <span class="preprocessor"></span>}
<a name="l00269"></a>00269 <span class="preprocessor">#endif</span>
<a name="l00270"></a>00270 <span class="preprocessor"></span>
<a name="l00271"></a>00271 <span class="preprocessor">#endif</span>
<a name="l00272"></a>00272 <span class="preprocessor"></span>
<a name="l00273"></a>00273 
<a name="l00274"></a>00274 
</pre></div></div>
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