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--- biac:cluster:examples:featlevel1 [2014/08/04 16:03]
127.0.0.1 external edit
+++ biac:cluster:examples:featlevel1 [2023/02/23 18:43]
@@ Line 1: / Line 1: @@
-====== FEAT Level 1 Example Cluster Scripts ======
-These example scripts will allow you to run all of the FEAT level one analyses (intra-subject run-by-run) in parallel on the cluster.  The script "qsub_feat_level1" calls a cluster-friendly script called "qsub_feat_level1_onerun" for each of the runs in a session.  By running this way, all runs are submitted at the same time, which will decrease the amount of processing time it takes to get the first level results.
-As with previous FSL scripts, the 1st level template fsf file must first be created using the FEAT GUI and saved with keywords replacing any fields that are subject dependent.
-===== qsub_feat_level1 =====
-Example usage:
-<code>
-[user@head ~]$ ./qsub_feat_level1 99999
-Or, if the file has been set (using the "chmod" command) to have execute properties:
-[user@head ~]$ qsub_feat_level1 99999
-</code>
-Copy and edit code below:
-<code bash>
-#!/bin/bash
-# First input is exam number
-SUBJ=$1
-# Loop through the runs submitting a job to grid engine for each run
-for i in 01 02 03 04 05 06 07 08
-do
-# Call qsub_feat_level1_onerun
-# Creates an fsf file and runs feat on that fsf file for one run
-# Two input arguments:  Subject ID and run name
-qsub -v EXPERIMENT=Dummy.01 qsub_feat_level1_onerun $SUBJ run${i}
-done
-</code>
-===== qsub_feat_level1_onerun =====
-Example usage:
-<code>[user@head ~]$ qsub -v EXPERIMENT=Dummy.01 qsub_feat_level1_onerun 99999 run01</code>
-Copy and edit code below:
-<code bash>
-#!/bin/sh
-# This is a BIAC template script for jobs on the cluster
-# You have to provide the Experiment on command line
-# when you submit the job the cluster.
-#
-# >  qsub -v EXPERIMENT=Dummy.01  script.sh args
-#
-# There are 2 USER sections
-#  1. USER DIRECTIVE: If you want mail notifications when
-#     your job is completed or fails you need to set the
-#     correct email address.
-#
-#  2. USER SCRIPT: Add the user script in this section.
-#     Within this section you can access your experiment
-#     folder using $EXPERIMENT. All paths are relative to this variable
-#     eg: $EXPERIMENT/Data $EXPERIMENT/Analysis
-#     By default all terminal output is routed to the " Analysis "
-#     folder under the Experiment directory i.e. $EXPERIMENT/Analysis
-#     To change this path, set the OUTDIR variable in this section
-#     to another location under your experiment folder
-#     eg: OUTDIR=$EXPERIMENT/Analysis/GridOut
-#     By default on successful completion the job will return 0
-#     If you need to set another return code, set the RETURNCODE
-#     variable in this section. To avoid conflict with system return
-#     codes, set a RETURNCODE higher than 100.
-#     eg: RETURNCODE=110
-#     Arguments to the USER SCRIPT are accessible in the usual fashion
-#     eg:  $1 $2 $3
-# The remaining sections are setup related and don't require
-# modifications for most scripts. They are critical for access
-# to your data
-# --- BEGIN GLOBAL DIRECTIVE --
-#$ -S /bin/sh
-#$ -o $HOME/$JOB_NAME.$JOB_ID.out
-#$ -e $HOME/$JOB_NAME.$JOB_ID.out
-#$ -m ea
-# -- END GLOBAL DIRECTIVE --
-# -- BEGIN PRE-USER --
-#Name of experiment whose data you want to access
-EXPERIMENT=${EXPERIMENT:?"Experiment not provided"}
-source /etc/biac_sge.sh
-EXPERIMENT=`biacmount $EXPERIMENT`
-EXPERIMENT=${EXPERIMENT:?"Returned NULL Experiment"}
-if [ $EXPERIMENT = "ERROR" ]
-then
-	exit 32
-else
-#Timestamp
-echo "----JOB [$JOB_NAME.$JOB_ID] START [`date`] on HOST [$HOSTNAME]----"
-# -- END PRE-USER --
-# **********************************************************
-# -- BEGIN USER DIRECTIVE --
-# Send notifications to the following address
-#$ -M user@somewhere.edu
-# -- END USER DIRECTIVE --
-# -- BEGIN USER SCRIPT --
-# User script goes here
-#Need to input EXPERIMENT, SUBJ and RUN NAME
-#Example qsub -v EXPERIMENT=Dummy.01 qsub_feat_level1_onerun 99999 run01
-SUBJ=$1
-RUN=$2
-#Set the directories
-FUNCDIR=$EXPERIMENT/Data/FSLFunc/$SUBJ
-BEHAVDIR=$EXPERIMENT/Data/Behav/$SUBJ/FSL/$RUN
-ANAT=$EXPERIMENT/Data/$SUBJ/anat_brain.nii.gz
-TEMPLATEDIR=$EXPERIMENT/Scripts/FSL
-OUTDIR=$EXPERIMENT/Analysis/FSL/$SUBJ
-#Set some variables
-OUTPUT=$OUTDIR/$RUN
-DATA=$FUNCDIR/$RUN/${RUN}.hdr
-ORIENT=$FUNCDIR/ORIENT.mat
-TARG=$BEHAVDIR/Targ.stf
-NEUT=$BEHAVDIR/NeutCorr.stf
-SCARY=$BEHAVDIR/ScaryCorr.stf
-mkdir -p $OUTDIR
-cd $TEMPLATEDIR
-#Makes the fsf file using the template
-for i in 'template.fsf'; do
-sed -e 's@OUTPUT@'$OUTPUT'@g' \
--e 's@ANAT@'$ANAT'@g' \
--e 's@ORIENT@'$ORIENT'@g' \
--e 's@TARG@'$TARG'@g' \
--e 's@NEUT@'$NEUT'@g' \
--e 's@SCARY@'$SCARY'@g' \
--e 's@FSLDIR@'$FSLDIR'@g' \
--e 's@DATA@'$DATA'@g' <$i> ${OUTDIR}/FEAT_${RUN}.fsf
-done
-#Run feat analysis
-feat ${OUTDIR}/FEAT_${RUN}.fsf
-# -- END USER SCRIPT -- #
-# **********************************************************
-# -- BEGIN POST-USER --
-echo "----JOB [$JOB_NAME.$JOB_ID] STOP [`date`]----"
-OUTDIR=${OUTDIR:-$EXPERIMENT/Analysis}
-mv $HOME/$JOB_NAME.$JOB_ID.out $OUTDIR/$JOB_NAME.$JOB_ID.out
-RETURNCODE=${RETURNCODE:-0}
-exit $RETURNCODE
-fi
-# -- END POST USER--
-</code>

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