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<h1 class="mume-header" id="ljh_fs_lr164k2fs_lr32k%E5%87%BD%E6%95%B0%E8%AF%B4%E6%98%8E">LJH_fs_LR164k2fs_LR32k函数说明</h1>
<h2 class="mume-header" id="%E5%87%BD%E6%95%B0ljh_fs_lr164k2fs_lr32ksh">函数：LJH_fs_LR164k2fs_LR32k.sh</h2>
<h3 class="mume-header" id="%E8%83%8C%E6%99%AF%E4%BB%8B%E7%BB%8D">背景介绍</h3>
<p><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext>    </mtext></mrow><annotation encoding="application/x-tex">~~~~</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0em;vertical-align:0em;"></span><span class="mspace nobreak"> </span><span class="mspace nobreak"> </span><span class="mspace nobreak"> </span><span class="mspace nobreak"> </span></span></span></span>Surface数据有不同的template,目前广泛使用的两种MNI空间下的surface的template是<a href="https://surfer.nmr.mgh.harvard.edu/">freesurfer</a>的fsaverage系列和HCP使用的fs_LR系列,可以认为这是两种不同的<strong>surface space</strong>。<br>
<span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext>    </mtext></mrow><annotation encoding="application/x-tex">~~~~</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0em;vertical-align:0em;"></span><span class="mspace nobreak"> </span><span class="mspace nobreak"> </span><span class="mspace nobreak"> </span><span class="mspace nobreak"> </span></span></span></span> fsaverage系列主要有5种：fsaverage,fsaverage3,fsaverage4,fsaverage5,fsaverage6。这些template的形状都相同,只是采样点不同，freesurfer的recon-all使用的fsaverage采样点数为164k。<br>
<span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext>    </mtext></mrow><annotation encoding="application/x-tex">~~~~</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0em;vertical-align:0em;"></span><span class="mspace nobreak"> </span><span class="mspace nobreak"> </span><span class="mspace nobreak"> </span><span class="mspace nobreak"> </span></span></span></span>fs_LR系列常见的主要有fs_LR164k和fs_LR32k，它们的区别也仅仅只是采样点数不同。<br>
<span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext>    </mtext></mrow><annotation encoding="application/x-tex">~~~~</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0em;vertical-align:0em;"></span><span class="mspace nobreak"> </span><span class="mspace nobreak"> </span><span class="mspace nobreak"> </span><span class="mspace nobreak"> </span></span></span></span>在实际问题中，经常需要实现这<strong>两种surface space之间的数据的比较与mapping</strong>，或者<strong>同surface space下不同的采样率的surface之间的数据的转换</strong>，或者需要把数据统一map到同一个surface space以便进一步统计分析。因此，这两种surface space之间的的数据的resample至关重要。</p>
<h3 class="mume-header" id="%E5%87%BD%E6%95%B0%E7%9A%84%E4%B8%BB%E8%A6%81%E5%8A%9F%E8%83%BD">函数的主要功能</h3>
<p><span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext>    </mtext></mrow><annotation encoding="application/x-tex">~~~~</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0em;vertical-align:0em;"></span><span class="mspace nobreak"> </span><span class="mspace nobreak"> </span><span class="mspace nobreak"> </span><span class="mspace nobreak"> </span></span></span></span><strong>fs_LR164k下的metric数据下采样到fs_LR32k space。</strong></p>
<h3 class="mume-header" id="%E8%BF%90%E8%A1%8C%E7%8E%AF%E5%A2%83%E8%A6%81%E6%B1%82">运行环境要求</h3>
<ul>
<li><strong>软件及系统</strong>：函数为Bash脚本，建议linux，resample主要命令来自软件<a href="https://www.humanconnectome.org/software/connectome-workbench">workbench</a>。</li>
</ul>
<h3 class="mume-header" id="%E5%87%BD%E6%95%B0%E8%AF%B4%E6%98%8E">函数说明</h3>
<ul>
<li>
<p><strong>函数编写思路</strong><br>
fs_LR164k下任意space下的metric，会先resample到fsaverage上，然后再从fsaverage下配到fs_LR32k上。其调用的子函数 <em><strong>fsave2fs_LR32k.sh</strong></em>,主要功能是把Metric数据从fsaverage配到fs_LR32k。采用这种方式主要是因为freesurfer和fs_LR标准的template之间的变换文件比较齐全，借助freesurfe的fsaverage作为桥梁可以很方便实现转换。</p>
</li>
<li>
<p><strong>函数调用</strong><br>
<strong>bash LJH_fs_LR164k2fs_LR32k.sh input1 input2 input3</strong></p>
</li>
<li>
<p><strong>函数的输入输出</strong></p>
<ul>
<li>
<p><em><strong>Inputs</strong></em><br>
<strong>input1</strong>:The gifti format file in fs_LR164k space.（fs_LR164空间下的func.gii文件路径）<br>
<strong>input2</strong>:The hemi of the surf,it should be "L" or "R".（半球控制参数）<br>
<strong>input3</strong>:The output name of the file registerd to fs_LR32k space.（配准到fs_LR32k的结果文件路径）</p>
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<p><em><strong>Outputs</strong></em><br>
<span class="katex"><span class="katex-mathml"><math xmlns="http://www.w3.org/1998/Math/MathML"><semantics><mrow><mtext>    </mtext></mrow><annotation encoding="application/x-tex">~~~~</annotation></semantics></math></span><span class="katex-html" aria-hidden="true"><span class="base"><span class="strut" style="height:0em;vertical-align:0em;"></span><span class="mspace nobreak"> </span><span class="mspace nobreak"> </span><span class="mspace nobreak"> </span><span class="mspace nobreak"> </span></span></span></span>The overlay matric registered to fs_LR32k space.</p>
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</ul>
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<p><strong>函数调用示例</strong></p>
<pre class="language-text"> ## bash Code demo.
bash /data/disk2/luojunhao/Hill_PNAS10_Figure_4/CuiZaixu/LJHCode/fs_LR164k2fs_LR32k.sh /data/disk2/luojunhao/Hill_PNAS10_Figure_4/CuiZaixu/PALS-term12_and_B12_SurfaceAREA_Percentage_SUMMARY.surface_shape_onLR_L.func.gii L /data/disk2/luojunhao/Hill_PNAS10_Figure_4/CuiZaixu/espansion_164k_32k_func/PALS-term12_and_B12_SurfaceAREA_Percentage_SUMMARY.surface_shape_onLR_fs_LR32k.L.func.gii
</pre>
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</ul>
<h3 class="mume-header" id="%E5%8F%82%E8%80%83%E6%9D%90%E6%96%99">参考材料</h3>
<p><a href="http://freesurfer.net/fswiki/mri_surf2surf">mri_surf2surf</a><br>
<a href="https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-9.HowdoImapdatabetweenFreeSurferandHCP?">HCP Users FAQ9:How do I map data between FreeSurfer and HCP?</a></p>
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