diff --git a/rubix_parallel.sh b/rubix_parallel.sh index f7024946b4cdd003b144b209e52e9b981587a5f8..d83e36989c2703050e7de6f8233457a0efa7db38 100644 --- a/rubix_parallel.sh +++ b/rubix_parallel.sh @@ -179,7 +179,7 @@ else fi fi fi -exit 1 + echo Making rubix directory structure mkdir -p ${subjdir}.rubiX @@ -200,11 +200,11 @@ echo Queuing parallel processing stage if [ ${gflag} -eq 1 ]; then opts="$opts --gLR=${subjdir}.rubiX/grad_devLR_slice_${slicezp} --gHR=${subjdir}.rubiX/grad_devHR_newslice_${slicezp}" fi - echo "$devel_dir/rubix --dLR=${subjdir}.rubiX/dataLR_slice_${slicezp} --mLR=${subjdir}.rubiX/nodif_brain_maskLR_slice_${slicezp} --rLR=${subjdir}.rubiX/bvecsLR --bLR=${subjdir}.rubiX/bvalsLR --dHR=${subjdir}.rubiX/dataHR_newslice_${slicezp} --rHR=${subjdir}.rubiX/bvecsHR --bHR=${subjdir}.rubiX/bvalsHR --forcedir --nf=$nfibres --nM=$nModes --bi=$burnin --model=$modelnum --logdir=${subjdir}.rubiX/diff_slices/data_slice_$slicezp ${opts}" >> ${subjdir}.rubiX/commands.txt + echo "$devel_dir/rubix --dLR=${subjdir}.rubiX/dataLR_slice_${slicezp} --mLR=${subjdir}.rubiX/nodif_brain_maskLR_slice_${slicezp} --rLR=${subjdir}.rubiX/bvecsLR --bLR=${subjdir}.rubiX/bvalsLR --dHR=${subjdir}.rubiX/dataHR_newslice_${slicezp} --rHR=${subjdir}.rubiX/bvecsHR --bHR=${subjdir}.rubiX/bvalsHR --forcedir --nf=$nfibres --nM=$nmodes --bi=$burnin --model=$model --logdir=${subjdir}.rubiX/diff_slices/data_slice_$slicezp ${opts}" >> ${subjdir}.rubiX/commands.txt slice=$(($slice + 1)) done RubiXid=`${FSLDIR}/bin/fsl_sub -T 1400 -j $preprocid -l ${subjdir}.rubiX/logs -N rubix -t ${subjdir}.rubiX/commands.txt` echo Queuing post processing stage - mergeid=`${FSLDIR}/bin/fsl_sub -T 60 -R 8000 -j $RubiXid -N rubix_post -l ${subjdir}.rubiX/logs $script_dir/rubix_postproc.sh ${subjdir} ${filterflag}` \ No newline at end of file + mergeid=`${FSLDIR}/bin/fsl_sub -T 60 -R 8000 -j $RubiXid -N rubix_post -l ${subjdir}.rubiX/logs $script_dir/rubix_postproc.sh ${subjdir} ${filterflag}`