When running trac-all -prep and including b0 inhomogeneity correction with epidewarp.fsl I get the following error.
Looking at the epidewarp.fsl source code I see that the error is occurring because of this section of the code.
set FSLVersion = `cat $FSLDIR/etc/fslversion`;
set FSLVerMaj = `echo $FSLVersion | cut -c 1`
echo FSLVersion $FSLVersion
echo FSLVerMaj $FSLVerMaj
if($FSLVerMaj == 3) then
set FSLPre = avw
set DilFlag = -dil
set FSLToFloat = avwmaths_32R
set FSLToFloatFlag = ()
else if($FSLVerMaj == 4) then
set FSLPre = fsl
set DilFlag = -dilM
set FSLToFloat = (fslmaths)
set FSLToFloatFlag = (-odt float)
else if($FSLVerMaj == 5) then
set FSLPre = fsl
set DilFlag = -dilM
set FSLToFloat = (fslmaths)
set FSLToFloatFlag = (-odt float)
else
echo "FSL Version is $FSLVersion, must be 3.X or 4.X or 5.X"
exit 1;
endif
Since fsl is now at version 6.0.1 would epidewarp.fsl be compatible with this version?
Could I simply include
else if($FSLVerMaj == 6) then
set FSLPre = fsl
set DilFlag = -dilM
set FSLToFloat = (fslmaths)
set FSLToFloatFlag = (-odt float)
or are these paramaters different under fsl 6.x+?
Best,