From 494227dafa462da39bc43623426a435eaa0684d3 Mon Sep 17 00:00:00 2001
From: FSL Automated Build Engineer <cowboy@fmrib.ox.ac.uk>
Date: Fri, 29 Aug 2008 15:26:30 +0000
Subject: [PATCH] Removed old bedpost
---
old_bedpostX | 264 -------------------------------------------
old_bedpost_kill_all | 14 ---
old_bedpost_kill_pid | 21 ----
old_bedpost_proc | 39 -------
probtrack.cc | 77 -------------
probtrack.h | 13 ---
6 files changed, 428 deletions(-)
delete mode 100644 old_bedpostX
delete mode 100755 old_bedpost_kill_all
delete mode 100755 old_bedpost_kill_pid
delete mode 100755 old_bedpost_proc
delete mode 100644 probtrack.cc
delete mode 100644 probtrack.h
diff --git a/old_bedpostX b/old_bedpostX
deleted file mode 100644
index d3f3935..0000000
--- a/old_bedpostX
+++ /dev/null
@@ -1,264 +0,0 @@
-#!/bin/sh
-
-# SHCOPYRIGHT
-
-if [ "x$SGE_ROOT" != "x" ] && [ -f $FSLDIR/bin/sge_bedpostX ] ; then
- exec $FSLDIR/bin/sge_bedpostX $@
-fi
-
-Usage() {
- echo ""
- echo "Usage: bedpostX <subject directory> [options]"
- echo ""
- echo "expects to find bvals and bvecs in subject directory"
- echo "expects to find data nodif_brain_mask nodif in subject directory"
- echo "options:"
- echo "-n (number of fibres per voxel, default 2)"
- echo "-w (ARD weight, more weight means less fibres killed per voxel, default 1)"
- echo "-b (burnin period, default 1000)"
- echo ""
- exit
-}
-
-trap Clean_Exit 2
-
-
-Clean_Exit(){
-
- if [ -d ${subjdir}.bedpostX/logs/pid_${$} ];then
- i=`ls ${subjdir}.bedpostX/logs/pid_${$}`
- for j in ${i};do
- host=`echo $j | awk -F _fdt_ '{print $1}'`
- pid=`echo $j | awk -F _fdt_ '{print $2}'`
- if [ "x${FSLMACHINELIST}" != "x" ]; then
-# ${FSLREMOTECALL} $host "kill -KILL $pid" #this leaves one child process per processor - what can you do?
- echo "if [ -r /usr/local/etc/fslconf/fsl.sh ];then . /usr/local/etc/fslconf/fsl.sh;fi; if [ -r /etc/fslconf/fsl.sh ];then . /etc/fslconf/fsl.sh;fi; if [ -r \${HOME}/.fslconf/fsl.sh ]; then . \${HOME}/.fslconf/fsl.sh; fi; if [ x\${FSLDIR} != "x" ];then \${FSLDIR}/bin/bedpostX_kill_pid ${pid} >/dev/null 2>&1; else echo FSLDIR not set in any default location on machine `hostname`;fi" | $FSLREMOTECALL $host /bin/sh >/dev/null 2>&1 &
- else
- ${FSLDIR}/bin/bedpostX_kill_pid ${pid}
- fi
- rm ${subjdir}.bedpostX/logs/pid_${$}/${j}
- done
- fi
- ExitUnlock;
-}
-
-Lock(){
- if [ "x${FSLLOCKDIR}" != "x" ];then
- touch ${FSLLOCKDIR}/.bedpostX.lock
- fi
-}
-
-ExitUnlock(){
- if [ -f ${FSLLOCKDIR}/.bedpostX.lock ];then
- rm ${FSLLOCKDIR}/.bedpostX.lock
- fi
-
- #clean up slices
- ndat_sl=`echo ${subjdir}/data_slice_* | grep -v "slice_\*" |wc -w`
- nnodif_sl=`echo ${subjdir}/nodif_brain_mask_slice_* | grep -v "slice_\*" |wc -w`
- if [ $ndat_sl -ge 0 ] ;then
- rm -f ${subjdir}/data_slice_*
- fi
-
- if [ $nnodif_sl -ge 0 ] ;then
- rm -f ${subjdir}/nodif_brain_mask_slice_*
- fi
-
- exit
-}
-
-LockTest(){
- if [ "x${FSLLOCKDIR}" = "x" ];then
- echo 1;
- elif [ ! -f ${FSLLOCKDIR}/.bedpostX.lock ];then
- echo 1;
- else
- echo 0;
- fi
-}
-
-make_absolute(){
- dir=$1;
- if [ -d ${dir} ]; then
- OLDWD=`pwd`
- cd ${dir}
- dir_all=`pwd`
- cd $OLDWD
- else
- dir_all=${dir}
- fi
- echo ${dir_all}
-}
-
-
-
-[ "$1" = "" ] && Usage
-
-if [ `LockTest` -eq 0 ]; then
- echo "bedpostX is currently being run - try again later"
- exit
-fi
-
-if [ "x${FSLMACHINELIST}" != "x" ];then
- if [ "x${FSLREMOTECALL}" = "x" ];then
- echo "error: you must set FSLREMOTECALL if you have set FSLMACHINELIST"
- exit
- fi
-fi
-
-Lock;
-
-
-subjdir=`make_absolute $1`
-subjdir=`echo $subjdir | sed 's/\/$/$/g'`
-
-echo subjectdir is $subjdir
-
-#check that all required files exist
-
-
-if [ ! -d $subjdir ]; then
- echo "subject directory $1 not found"
- ExitUnlock
-fi
-
-if [ ! -f ${subjdir}/bvecs ]; then
- echo "${subjdir}/bvecs not found"
- ExitUnlock
-fi
-
-if [ ! -f ${subjdir}/bvals ]; then
- echo "${subjdir}/bvals not found"
- ExitUnlock
-fi
-
-if [ `${FSLDIR}/bin/imtest ${subjdir}/data` -eq 0 ]; then
- echo "${subjdir}/data not found"
- ExitUnlock
-fi
-
-if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif` -eq 0 ]; then
- echo "${subjdir}/nodif not found"
- ExitUnlock
-fi
-
-if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
- echo "${subjdir}/nodif_brain_mask not found"
- ExitUnlock
-fi
-
-
-#parse option arguments
-nfibres=2
-fudge=1
-burnin=1000
-while [ ! -z "$2" ]
-do
- case "$2" in
- -n) nfibres=$3;shift;;
- -w) fudge=$3;shift;;
- -b) burnin=$3;shift;;
- *) break;;
- esac
- shift
-done
-
-
-echo making bedpostX directory
-mkdir -p ${subjdir}.bedpostX/
-mkdir -p ${subjdir}.bedpostX/diff_slices
-
-echo copying files to bedpostX directory
-cp ${subjdir}/bvecs ${subjdir}/bvals ${subjdir}.bedpostX
-${FSLDIR}/bin/imcp ${subjdir}/nodif ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX
-${FSLDIR}/bin/fslmaths ${subjdir}/nodif -mas ${subjdir}/nodif_brain_mask ${subjdir}.bedpostX/nodif_brain
-
-
-mkdir -p ${subjdir}.bedpostX/logs
-mkdir -p ${subjdir}.bedpostX/logs/pid_${$}
-
-nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
-
-${FSLDIR}/bin/fslslice ${subjdir}/data
-${FSLDIR}/bin/fslslice ${subjdir}/nodif_brain_mask
-
-#for parallel processing, the following need to be setup elsewhere
-#FSLMACHINELIST="list of machines (can be duplicated for two processors etc.)"
-#FSLREMOTECALL="ssh (or rsh or whatever you want to use)"
-
-if [ "x$FSLMACHINELIST" = "x" ] ; then
- echo "processing data on local host"
- ${FSLDIR}/bin/bedpostX_proc $subjdir $nslices -n $nfibres -w $fudge -b $burnin ${subjdir}.bedpostX/logs/pid_${$} &
-else
- echo "processing data on hosts: $FSLMACHINELIST"
- for machine in $FSLMACHINELIST; do
- echo "if [ -r /usr/local/etc/fslconf/fsl.sh ];then . /usr/local/etc/fslconf/fsl.sh;fi; if [ -r /etc/fslconf/fsl.sh ];then . /etc/fslconf/fsl.sh;fi; if [ -r \${HOME}/.fslconf/fsl.sh ]; then . \${HOME}/.fslconf/fsl.sh; fi; if [ x\${FSLDIR} != "x" ];then \${FSLDIR}/bin/bedpostX_proc $subjdir $nslices ${subjdir}.bedpostX/logs/pid_${$}; else echo FSLDIR not set in any default location on machine `hostname`;fi"| $FSLREMOTECALL $machine /bin/sh &
- done
-fi
-echo finished
-
-b=0
-finished=0;
-while [ $finished -eq 0 ];do
- b=`expr $b + 1 `
- sleep 60;
- nfin=`echo ${subjdir}.bedpostX/logs/.*_finished | grep -v ".\*" |wc -w`
- if [ $nfin -eq $nslices ];then
- finished=1;
- fi
- if [ $b -eq 10 ]; then
- echo "$nfin slices processed"
- b=0
- fi
-done
-
-#postprocessing
-#postprocess $subjdir
-
-
-numfib=`${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_0000/f*samples |wc -w`
-echo number of fibres $numfib
-
-fib=1;
-while [ $fib -le $numfib ];do
- ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_th${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/th${fib}samples`
- ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_ph${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/ph${fib}samples`
- ${FSLDIR}/bin/fslmerge -z ${subjdir}.bedpostX/merged_f${fib}samples `${FSLDIR}/bin/imglob ${subjdir}.bedpostX/diff_slices/data_slice_*/f${fib}samples`
- ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_th${fib}samples -Tmean ${subjdir}.bedpostX/mean_th${fib}samples
- ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_ph${fib}samples -Tmean ${subjdir}.bedpostX/mean_ph${fib}samples
- ${FSLDIR}/bin/fslmaths ${subjdir}.bedpostX/merged_f${fib}samples -Tmean ${subjdir}.bedpostX/mean_f${fib}samples
-
- ${FSLDIR}/bin/make_dyadic_vectors ${subjdir}.bedpostX/merged_th${fib}samples ${subjdir}.bedpostX/merged_ph${fib}samples ${subjdir}.bedpostX/nodif_brain_mask ${subjdir}.bedpostX/dyads${fib}
-
- fib=`echo "$fib +1"|bc`;
-done
-
-echo Removing intermediate files
-
-if [ `imtest ${subjdir}.bedpostX/merged_th1samples` -eq 1 ];then
- if [ `imtest ${subjdir}.bedpostX/merged_ph1samples` -eq 1 ];then
- if [ `imtest ${subjdir}.bedpostX/merged_f1samples` -eq 1 ];then
- rm -rf ${subjdir}.bedpostX/diff_slices
- rm -f ${subjdir}/data_slice_*
- rm -f ${subjdir}/nodif_brain_mask_slice_*
- fi
- fi
-fi
-
-echo Creating identity xfm
-
-xfmdir=${subjdir}.bedpostX/xfms
-mkdir -p $xfmdir
-echo 1 0 0 0 > ${xfmdir}/eye.mat
-echo 0 1 0 0 >> ${xfmdir}/eye.mat
-echo 0 0 1 0 >> ${xfmdir}/eye.mat
-echo 0 0 0 1 >> ${xfmdir}/eye.mat
-
-echo Done
-
-ExitUnlock
-
-
-
-
-
diff --git a/old_bedpost_kill_all b/old_bedpost_kill_all
deleted file mode 100755
index 53e39f5..0000000
--- a/old_bedpost_kill_all
+++ /dev/null
@@ -1,14 +0,0 @@
-#!/bin/sh
-
-# Copyright (C) 2004 University of Oxford
-#
-# SHCOPYRIGHT
-
-j=`ps -U $USER |grep -v grep | grep bedpost|grep -v bedpost_kill | awk '{print $1}'`
-if [ "x${j}" != "x" ];then
- kill -KILL $j
-fi
-i=`ps -U $USER |grep -v grep | grep diff_pvm| awk '{print $1}'`
-if [ "x${i}" != "x" ];then
- kill -KILL $i
-fi
diff --git a/old_bedpost_kill_pid b/old_bedpost_kill_pid
deleted file mode 100755
index eefc6ad..0000000
--- a/old_bedpost_kill_pid
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/bin/sh
-
-# Copyright (C) 2004 University of Oxford
-#
-# SHCOPYRIGHT
-
-Usage(){
- echo "bedpost_kill_pid <pid>"
- echo ""
- echo "<pid> is the pid of the bedpost_proc"
- echo "kills this process + all diff_pvm children"
- echo ""
- exit
-}
-
-[ "$1" = "" ] && Usage
-pid=$1
-
-i=`ps -fU $USER |grep -v grep | grep diff_pvm |grep ${pid}| awk '{print $2}'`
-kill -KILL $pid $i
-
diff --git a/old_bedpost_proc b/old_bedpost_proc
deleted file mode 100755
index 9c677c8..0000000
--- a/old_bedpost_proc
+++ /dev/null
@@ -1,39 +0,0 @@
-#!/bin/sh
-
-# Copyright (C) 2004 University of Oxford
-#
-# SHCOPYRIGHT
-
-Usage() {
- echo ""
- echo "Usage: bedpost_proc <subject_dir> <nslices> [piddir]"
- echo ""
- exit
-}
-
-
-[ "$2" = "" ] && Usage
-[ "$3" = "" ] || touch ${3}/`hostname`_fdt_${$}
-
-
-subjdir=$1
-nslices=$2
-
-
-
-slice=0
-while [ $slice -lt $nslices ];do
- slicezp=`${FSLDIR}/bin/zeropad $slice 4`
- if [ ! -f ${subjdir}.bedpost/logs/.$slicezp ] ; then
- echo `hostname`_${$} > ${subjdir}.bedpost/logs/.$slicezp
- sleep 10
- if [ `hostname`_${$} = `cat ${subjdir}.bedpost/logs/.$slicezp | sed -n '1p'` ] ; then
- nice ${FSLDIR}/bin/diff_pvm --data=${subjdir}/data_slice_$slicezp --mask=${subjdir}/nodif_brain_mask_slice_$slicezp -b ${subjdir}/bvals -r ${subjdir}/bvecs --logdir=${subjdir}.bedpost/diff_slices/data_slice_$slicezp --nj=1300 --bi=300 --se=20 > ${subjdir}.bedpost/logs/log$slicezp
- touch ${subjdir}.bedpost/logs/.${slicezp}_finished
- fi
- fi
- slice=`echo "$slice + 1" | bc`
-done
-
-[ "$3" = "" ] || rm ${3}/`hostname`_fdt_${$}
-sleep 10
\ No newline at end of file
diff --git a/probtrack.cc b/probtrack.cc
deleted file mode 100644
index 2c40be1..0000000
--- a/probtrack.cc
+++ /dev/null
@@ -1,77 +0,0 @@
-/* Copyright (C) 2004 University of Oxford */
-
-/* CCOPYRIGHT */
-
-#include <iostream>
-#include <fstream>
-#include "newimage/newimageall.h"
-#include "utils/log.h"
-#include "meshclass/meshclass.h"
-#include "probtrack.h"
-
-
-using namespace std;
-using namespace NEWIMAGE;
-using namespace TRACT;
-using namespace Utilities;
-using namespace PARTICLE;
-using namespace TRACTVOLS;
-using namespace mesh;
-//using namespace NEWMAT;
-//////////////////////////
-/////////////////////////
-
-
-
-
-int main ( int argc, char **argv ){
- probtrackOptions& opts =probtrackOptions::getInstance();
- Log& logger = LogSingleton::getInstance();
- opts.parse_command_line(argc,argv,logger);
- srand(opts.rseed.value());
- if(opts.verbose.value()>0){
- opts.status();
- }
- if(opts.mode.value()=="simple")
- track();
- else if(opts.mode.value()=="seeds_to_targets")
- seeds_to_targets();
- else if(opts.mode.value()=="seedmask")
- alltracts();
- else if(opts.mode.value()=="twomasks_symm")
- twomasks_symm();
- else if(opts.mode.value()=="waypoints")
- waypoints();
- else if(opts.mode.value()=="matrix1")
- matrix1();
- else if(opts.mode.value()=="matrix2"){
- if(opts.meshfile.value()=="")
- matrix2();
- else
- mesh_matrix2();
- }
- else if(opts.mode.value()=="maskmatrix")
- maskmatrix();
- else if(opts.mode.value()=="meshlengths")
- mesh_lengths();
- else{
- cout <<"Invalid setting for option mode -- try setting mode=help"<<endl;
- }
-
- return 0;
-}
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
diff --git a/probtrack.h b/probtrack.h
deleted file mode 100644
index 019a223..0000000
--- a/probtrack.h
+++ /dev/null
@@ -1,13 +0,0 @@
-/* Copyright (C) 2004 University of Oxford */
-
-/* CCOPYRIGHT */
-
-#include "probtrackOptions.h"
-#include "particle.h"
-#include "tractvols.h"
-#include "pt_simple.h"
-#include "pt_twomasks.h"
-#include "pt_seeds_to_targets.h"
-#include "pt_alltracts.h"
-#include "pt_matrix.h"
-#include "pt_matrix_mesh.h"
--
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