====== fMRIPrep ======


<WRAP box round important>
**Development Paused**
 - resource required is too high for limited time of usefulness on Rocket 
</WRAP>


> fMRIPrep is a NiPreps (NeuroImaging PREProcessing toolS) application (www.nipreps.org) for the preprocessing of task-based and resting-state functional MRI (fMRI).

   * https://fmriprep.org/en/stable/index.html

===== Installation ======

You do **not** need Docker or other container tools in order to use fMRIPrep. The installation is quite simple using standard Python //venv// tools, as available on our HPC facilities.

<code lang=bash>
#!/bin/bash

DEST_DIR=/nobackup/njps3/fmriprep

# Load software modules needed to build
echo "Loading HPC software modules..."
module load Python/3.11.3-GCCcore-12.3.0 
module load CMake
module load Autoconf
module load Automake
module load GCC
echo "- Ok"
echo ""

# Create virtual environment to install dependencies
echo "Creating installation folder..."
python -m venv ${DEST_DIR}
mkdir -p ${DEST_DIR}/downloads
echo "- Your fmriprep software will all be installed under: ${DEST_DIR}"
echo "- Downloads will all be stored under: ${DEST_DIR}/downloads"
echo ""

echo "Activate new installation folder environment..."
echo "- Before: python was `which python3`"
echo "- Before: pip was `which pip3`"
source ${DEST_DIR}/bin/activate
echo "- After: python is now `which python3`"
echo "- After: pip is now `which pip3`"
echo ""

# Install fmriprep dependencies
echo "Installing requirements..."
echo "- This may take a while......."
echo ""

############################################
# FSL
############################################
echo "Downloading FSL..."
cd ${DEST_DIR} ; wget -nc -q https://fsl.fmrib.ox.ac.uk/fsldownloads/fslconda/releases/fslinstaller.py -O ${DEST_DIR}/downloads/fslinstaller.py 
if [ -s "$DEST_DIR/downloads/fslinstaller.py" ]
then
	echo "- Running FSL installation..."
	echo "- Ok"
	echo ""	
else
	echo "- ERROR - Cannot run FSL installation..."
	exit 1
fi

############################################
# ANTS
############################################
echo "Downloading ANTs..."
cd ${DEST_DIR} ; git clone -q https://github.com/ANTsX/ANTs.git
if [ -d "${DEST_DIR}/ANTs" ]
then
	echo "- Running ANTs installation..."
#mkdir ants-build
#cd ants-build
#cmake -DCMAKE_INSTALL_PREFIX=${DEST_DIR} ../ANTs
#make -j 4
#cd ANTS-build
#make install
	echo "- Ok"
	echo ""
else
	echo "- ERROR - Cannot run ANTs installation..."
	exit 1
fi

############################################
# Motif - needed for AFNI
############################################
echo "Downloading Motif..."
cd ${DEST_DIR} ; wget -nc -q https://sourceforge.net/projects/motif/files/Motif%202.3.8%20Source%20Code/motif-2.3.8.tar.gz/download -O ${DEST_DIR}/downloads/motif.tgz
if [ -s "${DEST_DIR}/downloads/motif.tgz" ]
then
	if [ -s "${DEST_DIR}/lib/libXm.so.4.0.4" ]
	then
		echo "- Motif already installed at ${DEST_DIR}/lib/libXm.so.4.0.4"
		echo "- Ok"
		echo ""
	else
		if [ -s "${DEST_DIR}/motif-2.3.8/README" ]
		then
			echo "- Motif src already unpacked"
		else
			echo "- Unpacking Motif src..."
			cd ${DEST_DIR} && tar xfz ${DEST_DIR}/downloads/motif.tgz
			if [ "$?" = "0" ]
			then
				echo "- Ok"
				echo ""
			else
				echo "- ERROR - Unpacking Motif src failed..."		
				exit 1
			fi
		fi		
		echo "- Installing Motif..."
		module purge
		module load Autoconf
		module load GCC
		module load make
		module load X11
		module load flex
		cd ${DEST_DIR}/motif-2.3.8 && ./configure --prefix=${DEST_DIR}
	
		# THe old Motif package has loads of bugs, here is one that stops it compiling:
		# https://www.linuxquestions.org/questions/linux-enterprise-47/error-when-compling-motif-4175669180/
		# https://bugs.gentoo.org/592868

		# Inject "%option main" to the top of wmluiltok.l		
		# To fix the compile bug referenced above
		grep "option main" tools/wml/wmluiltok.l 2>/dev/null
		if [ "$?" = "0" ]
		then
			echo "- Already patched with compile fix..."
		else
			echo "- Adding compile fix patch..."
			sed -i '1s/^/%option main\n /' tools/wml/wmluiltok.l
		fi

		make && make install
		if [ "$?" = "0" ]
		then
			echo "- Ok"
			echo ""
		else
			echo "- ERROR - installation failed..."		
			exit 1
		fi
	fi
else
	echo "- ERROR - Cannot run Motif installation..."
	exit 1
fi

############################################
# AFNI
############################################
echo "Downloading AFNI..."
cd ${DEST_DIR} ; wget -nc -q https://afni.nimh.nih.gov/pub/dist/tgz/afni_src.tgz -O ${DEST_DIR}/downloads/afni_src.tgz
if [ -s "${DEST_DIR}/downloads/afni_src.tgz" ]
then
	if [ -s "${DEST_DIR}/bin/afni" ]
	then
		echo "- AFNI already installed at ${DEST_DIR}/bin/afni"
		echo "- Ok"
		echo ""
	else

		if [ -s "${DEST_DIR}/afni_src/Makefile.linux_openmp_64" ]
		then
			echo "- AFNI src already unpacked"
		else
			echo "- Unpacking AFNI src..."
			cd ${DEST_DIR} && tar xfz ${DEST_DIR}/downloads/afni_src.tgz
			if [ "$?" = "0" ]
			then
				echo "- Ok"
				echo ""
			else
				echo "- ERROR - Unpacking AFI src failed..."		
				exit 1
			fi
		fi

		echo "- Running AFNI installation..."	
		cd afni_src
		module purge
		module load GCC
		module load make
		module load X11
		#module load motif

		# The makefile is a bit broken.
		# It has a hardcoded to call /usr/bin/gcc ...
		# It has a non-standard parameter to gcc '-V'
		cat Makefile.linux_openmp_64 | \
			sed 's/\/usr\/bin\/gcc/gcc/g' | \
			sed 's/\-V\ 34//g' > Makefile.rocket
		make -f Makefile.rocket vastness
		if [ "$?" = "0" ]
		then
			echo "- Ok"
			echo ""
		else
			echo "- ERROR - installation failed..."		
			exit 1
		fi
	fi
else
	echo "- ERROR - Cannot run AFNI installation..."
	exit 1
fi

############################################
# Freesurfer
############################################
echo "Downloading Freesurfer (this takes a long time)..."
cd ${DEST_DIR} ; wget -nc -q https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-linux-centos7_x86_64-7.4.1.tar.gz -O ${DEST_DIR}/downloads/freesurfer.tgz
if [ -s "${DEST_DIR}/downloads/freesurfer.tgz" ]
then
	echo "- Running Freesurfer installation..."
	if [ "$?" = "0" ]
	then
		echo "- Ok"
		echo ""
	else
		echo "- ERROR - installation failed..."		
		exit 1
	fi
else
	echo "- ERROR - Cannot run Freesurfer installation..."
	exit 1
fi

##########################################
# glibc_2.18 for deno
# deno has a dependency on >=glibc2.18 - which is
# newer than Rocket has. For Comet or other
# newer platforms, this is NOT needed.
##########################################
echo "Downloading glibc (for deno runtime)..."
cd ${DEST_DIR} ; wget -nc -q https://ftp.gnu.org/gnu/glibc/glibc-2.41.tar.gz -O ${DEST_DIR}/downloads/glibc-2.41.tar.gz
if [ -s "${DEST_DIR}/glibc-2.41.tar.gz" ]
then
	if [ -s "${DEST_DIR}/lib/libc.so" ]
	then
		echo "- glibc is already installed at ${DEST_DIR}/lib/libc.so"
		echo "- Ok"
		echo ""
	else
		echo "- Running glibc installation..."
		echo "- LD_LIBRARY_PATH: $LD_LIBRARY_PATH"
		echo "- PWD: `pwd`"
		module purge
		module load Python/3.11.3-GCCcore-12.3.0 
		module load CMake
		module load Autoconf
		module load Automake
		module load GCC
		module load make
		tar xfz ${DEST_DIR}/downloads/glibc-2.41.tar.gz 
		cd ${DEST_DIR}/glibc-2.41 
		mkdir build
		cd build
		../configure --prefix=${DEST_DIR}/glibc
		make -j4
		make install
		if [ "$?" = "0" ]
		then
			echo "- Ok"
			echo ""
		else
			echo "- ERROR - installation failed..."		
			exit 1
		fi
	fi
else
	echo "- ERROR - Cannot run glibc installation..."
	exit 1
fi

##########################################
# deno
##########################################
echo "Downloading deno..." ; wget -nc -q https://github.com/denoland/deno/releases/download/v2.3.3/deno-x86_64-unknown-linux-gnu.zip -O ${DEST_DIR}/downloads/deno.zip
if [ -s "${DEST_DIR}/downloads/deno.zip" ]
then
	if [ -x "${DEST_DIR}/bin/deno" ]
	then
		echo "- deno is already installed at ${DEST_DIR}/bin/deno"
		echo "- Ok"
		echo ""
	else
		echo "- Unzipping deno..."
		cd ${DEST_DIR} && unzip ${DEST_DIR}/downloads/deno.zip && mv -fv ${DEST_DIR}/deno ${DEST_DIR}/bin/deno
		chmod +x ${DEST_DIR}/bin/deno
		if [ "$?" = "0" ]
		then
			echo "- Ok"
			echo ""
		else
			echo "- ERROR - installation failed..."		
			exit 1
		fi
	fi
else
	echo "- ERROR - Cannot unzip deno..."
	exit 1
fi

##########################################
# bids-validator
###########################################
echo "Installing bids-validator..."
module purge
module load Python/3.11.3-GCCcore-12.3.0 
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${DEST_DIR}/glibc
echo "- LD_LIBRARY_PATH: $LD_LIBRARY_PATH"
pip3 install bids-validator-deno 
if [ "$?" = "0" ]
then
	echo "- Ok"
	echo ""
else
	echo "- ERROR - Cannot install bids-validator"
	exit 1
fi

##########################################
# Connectome-workbench
##########################################
echo "Downloading connectome-workbench..."
cd ${DEST_DIR} ; wget -nc -q https://www.humanconnectome.org/storage/app/media/workbench/workbench-rh_linux64-v2.0.1.zip -O ${DEST_DIR}/downloads/workbench.zip
if [ -s "${DEST_DIR}/downloads/workbench.zip" ]
then
	echo "- Running connectome-workbench installation..."
	if [ "$?" = "0" ]
	then
		echo "- Ok"
		echo ""
	else
		echo "- ERROR - installation failed..."		
		exit 1
	fi
else
	echo "- ERROR - Cannot run connectome-workbench installation..."
	exit 1
fi
</code>

== Testing ==

===== Using Flower =====

----

[[:faq:index|Back to FAQ]]