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<section id="hcp-data-processing">
<h1>HCP data processing<a class="headerlink" href="#hcp-data-processing" title="Link to this heading"></a></h1>
<p>Note that HCP data processing was conducted on Katana. Therefore, some settings are specific to the platform. All the content can be found on <a class="reference external" href="https://github.com/Washington-University/HCPpipelines/wiki/Installation-and-Usage-Instructions">HCP Pipelines</a>, and <a class="reference external" href="https://github.com/physimals/hcp-asl">HCP ASL pipeline</a> webpages. This webpage is meant to record what I have done, what problems I encountered, and how I resolved them, for future replication and educating new students.</p>
<section id="software-installation">
<h2>Software installation<a class="headerlink" href="#software-installation" title="Link to this heading"></a></h2>
<p>Our first task in HCP-Aging data is to process ASL data. The <a class="reference external" href="https://github.com/physimals/hcp-asl">ASL pipeline</a> requires prerequisites of FSL (version >= 6.0.5.1), HCP workbench (version >= 1.5.0), HCP pipelines, and FreeSurfer (Note that version 6.0 and 5.3.0-HCP are compatible in <a class="reference external" href="https://github.com/Washington-University/HCPpipelines/wiki/Installation-and-Usage-Instructions#prerequisites">HCP pipeline prerequisites</a>). The installation of FSL, HCP workbench, and FreeSurfer are relatively straightforward.</p>
<p>The installation of <a class="reference external" href="https://github.com/Washington-University/HCPpipelines/wiki/Installation-and-Usage-Instructions#prerequisites">HCP pipeline requires a few prerequisites</a>. In these prerequisites, the installation of gradunwarp can follow <a class="reference external" href="https://github.com/Washington-University/gradunwarp">this page</a>. Note that <em>openblas</em> may need to be available. On Katana, this can be done by <code class="docutils literal notranslate"><span class="pre">module</span> <span class="pre">load</span> <span class="pre">openblass/0.3.21</span></code>. The installation of FSL FIX can follow <a class="reference external" href="https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FIX/UserGuide">this webpage</a>. In particular, R packages required by FIX can be installed by following the subsection below.</p>
<section id="r-packages-for-fsl-fix">
<h3>R packages for FSL FIX<a class="headerlink" href="#r-packages-for-fsl-fix" title="Link to this heading"></a></h3>
<p>Followed instruction in the end of <a class="reference external" href="https://github.com/Washington-University/HCPpipelines/blob/master/ICAFIX/README.md">this webpage</a>. It took me a full day to get this work!!!</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>module load r/4.2.2
export R_LIBS=/srv/scratch/cheba/Imaging/software/R_libs
# Temporarily rename FSL, otherwise it will interfere with installation
mv /srv/scratch/cheba/NiL/Software/fsl/6.0.6.5 /srv/scratch/cheba/NiL/Software/fsl/6.0.6.5_bak
R
install.packages('devtools', dependencies=TRUE)
require ('devtools')
quit()
PACKAGES="lattice_0.20-38 Matrix_1.2-15 survival_2.43-3 MASS_7.3-51.1 class_7.3-14 codetools_0.2-16 KernSmooth_2.23-15 mvtnorm_1.0-8 modeltools_0.2-22 zoo_1.8-4 sandwich_2.5-0 strucchange_1.5-1 TH.data_1.0-9 multcomp_1.4-8 coin_1.2-2 bitops_1.0-6 gtools_3.8.1 gdata_2.18.0 caTools_1.17.1.1 gplots_3.0.1 kernlab_0.9-24 ROCR_1.0-7 party_1.0-25 e1071_1.6-7 randomForest_4.6-12"
MIRROR="http://cloud.r-project.org"
for package in $PACKAGES
do
wget "$MIRROR"/src/contrib/Archive/$(echo "$package" | cut -f1 -d_)/"$package".tar.gz || \
wget "$MIRROR"/src/contrib/"$package".tar.gz
R CMD INSTALL "$package".tar.gz
done
</pre></div>
</div>
<p>An alternative approach is to follow the instructions in the README file in the downloaded fix.tar.gz. I haven’t tried this myself.</p>
</section>
</section>
<section id="setting-environment-variables">
<h2>Setting environment variables<a class="headerlink" href="#setting-environment-variables" title="Link to this heading"></a></h2>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span># HCP workbench
export PATH=$PATH:/srv/scratch/cheba/Imaging/software/workbench/bin_rh_linux
# HCP version of gredunwarp
conda activate gradunwarp
export PATH=$PATH:/srv/scratch/cheba/Imaging/software/gradunwarp-1.2.1/build/scripts.linux-x86_64-3.7
# MSM_HOCR
module load openblas/0.3.21
export PATH=$PATH:/srv/scratch/cheba/Imaging/software
# HCP pipelines
export HCPPIPEDIR=/srv/scratch/cheba/Imaging/software/HCPpipelines-4.7.0
# R for FSL FIX
module load r/4.2.2 matlab/R2019a
export R_LIBS=/srv/scratch/cheba/Imaging/software/R_libs
export FSL_FIX_R_CMD=$(which R)
# configure FSL FIX
export FSL_FIX_MATLAB_MODE=1
export FSL_FIX_WBC=/srv/scratch/cheba/Imaging/software/workbench/bin_rh_linux64/wb_command
cd /srv/scratch/cheba/Imaging/software
git clone https://github.com/Washington-University/cifti-matlab.git # clone cifti-matlab library from github.
# I am not sure if this will be the same as
# /srv/scratch/cheba/Imaging/software/HCPpipelines-4.7.0/global/matlab/cifti-matlab
# But to be safe, and also recommended in this link
# (https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ#HCPUsersFAQ-2.HowdoyougetCIFTIfilesintoMATLAB?),
# this library is cloned from GitHub.
export FSL_FIX_CIFTIRW=/srv/scratch/cheba/Imaging/software/cifti-matlab
cd /srv/scratch/cheba/Imaging/software/fix-v1.06.15
./setting.sh
</pre></div>
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</section>
<section id="to-do-list">
<h2>TO-DO list<a class="headerlink" href="#to-do-list" title="Link to this heading"></a></h2>
<ul class="simple">
<li><p>Go-through from <em>Usage</em> onwards on <a class="reference external" href="https://github.com/physimals/hcp-asl#installation">HCP ASL webpage</a>.</p></li>
<li><p>Go-through from <em>Getting example data</em> onwards on <a class="reference external" href="https://github.com/Washington-University/HCPpipelines/wiki/Installation-and-Usage-Instructions#getting-example-data">HCP pipelines webpage</a>.</p></li>
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