*** empty log message ***

Makefile

@@ -5,7 +5,6 @@ PROJNAME = fdt
 USRINCFLAGS = -I${INC_NEWMAT} -I${INC_NEWRAN} -I${INC_CPROB} -I${INC_PROB} -I${INC_ZLIB}
 USRLDFLAGS = -L${LIB_NEWMAT} -L${LIB_NEWRAN} -L${LIB_CPROB} -L${LIB_PROB} -L${LIB_ZLIB}
 
- 
 DLIBS = -lmeshclass -lbint -lnewimage -lutils -lmiscmaths -lnewmat -lnewran -lfslio -lniftiio -lznz -lcprob -lprob -lm -lz
 #DLIBS = -lbint -lnewimage -lutils -lmiscmaths  -lnewmat -lfslio -lniftiio -lznz -lcprob -lprob -lm -lz
 
@@ -48,7 +47,7 @@ TESTOBJS=testfile.o
 VECREGOBJS=vecreg.o
 
 SGEBEDPOST = bedpost bedpost_datacheck
-SGEBEDPOSTX = bedpostX bedpostX_postproc.sh bedpostX_preproc.sh bedpostX_single_slice.sh
+SGEBEDPOSTX = bedpostx bedpostx_postproc.sh bedpostx_preproc.sh bedpostx_single_slice.sh
 
 SCRIPTS = eddy_correct zeropad maskdyads ${SGEBEDPOST} ${SGEBEDPOSTX}
 FSCRIPTS = correct_and_average ocmr_preproc
@@ -58,7 +57,7 @@ XFILES = dtifit ccops probtrack find_the_biggest medianfilter diff_pvm make_dyad
 FXFILES = reord_OM sausages replacevols fdt_matrix_ops probtrackx indexer
 
 
-RUNTCLS = Fdt Fdtx
+RUNTCLS = Fdt
 
 all: ${XFILES} ${FXFILES} 
 
@@ -113,14 +112,3 @@ ${TEST}:    	${TESTOBJS}
 ${VECREG}:    	${VECREGOBJS}
 		   ${CXX} ${CXXFLAGS} ${LDFLAGS} -o $@ ${VECREGOBJS} ${DLIBS}
 
-
-
-
-
-
-
-
-
-
-
-

bedpost

 #!/bin/sh
 
-#   Copyright (C) 2004 University of Oxford
+#   Copyright (C) 2007 University of Oxford
 #
 #   SHCOPYRIGHT
 
-
 echo
-echo "Warning - bedpost has been deprecated! Please use bedpostX instead."
-[ -z "$@" ] && ${FSLDIR}/bin/bedpostX
-echo "Executing \"bedpostX $@ -n 1\" instead."
+echo "Error - bedpost has been superceded by bedpostx! Please instead run:"
+echo bedpostx $@ -n 1
 echo
-${FSLDIR}/bin/bedpostX $@ -n 1
+

bedpostx

@@ -14,7 +14,7 @@ fi
 
 Usage() {
     echo ""
-    echo "Usage: bedpostX <subject directory> [options]"
+    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"
@@ -93,7 +93,7 @@ if [ `${FSLDIR}/bin/imtest ${subjdir}/nodif_brain_mask` -eq 0 ]; then
 	exit 1
 fi
 
-echo Making bedpostX directory structure
+echo Making bedpostx directory structure
 
 mkdir -p ${subjdir}.bedpostX/
 mkdir -p ${subjdir}.bedpostX/diff_slices
@@ -103,19 +103,19 @@ mkdir -p ${subjdir}.bedpostX/xfms
 
 mailto=`whoami`@fmrib.ox.ac.uk
 echo Queuing preprocessing stages
-preprocid=`${FSLDIR}/bin/fsl_sub -F -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostX_preproc.sh ${subjdir}`
+preprocid=`${FSLDIR}/bin/fsl_sub -F -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_preproc.sh ${subjdir}`
 
 echo Queuing parallel processing stage
 nslices=`${FSLDIR}/bin/fslval ${subjdir}/data dim3`
 [ -f ${subjdir}.bedpostX/commands.txt ] && rm ${subjdir}.bedpostX/commands.txt
 for ((slice=0; slice < $nslices; slice++)) ; do
-    echo "${FSLDIR}/bin/bedpostX_single_slice.sh $subjdir $nfibres $fudge $burnin $slice" \
+    echo "${FSLDIR}/bin/bedpostx_single_slice.sh $subjdir $nfibres $fudge $burnin $slice" \
 	>> ${subjdir}.bedpostX/commands.txt
 done
 bedpostid=`${FSLDIR}/bin/fsl_sub -j $preprocid -l ${subjdir}.bedpostX/logs -M $mailto -N bedpostx -t ${subjdir}.bedpostX/commands.txt`
 
 echo Queuing post processing stage
-mergeid=`${FSLDIR}/bin/fsl_sub -j $bedpostid -F -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostX_postproc.sh $subjdir`
+mergeid=`${FSLDIR}/bin/fsl_sub -j $bedpostid -F -l ${subjdir}.bedpostX/logs ${FSLDIR}/bin/bedpostx_postproc.sh $subjdir`
 
 if [ "x$SGE_ROOT" != "x" ]; then
     echo