diff --git a/verbena.in b/verbena.in index cbfc273..8a10e2f 100644 --- a/verbena.in +++ b/verbena.in @@ -29,8 +29,9 @@ Usage() { echo " {-te} : TE (in s) {default: 0.065 s}" echo "" echo "Options:" + echo " -aifconc : AIF curve is a concentration curve rather than a signal curve" echo " -mv : Add a macro vascular component" - echo " -sigadd : Add MV component in signal domain (rather than concentrations)" + echo " -sigadd : Add MV component in signal domain (rather than concentrations)" echo " -modelfree : Run a 'model free' SVD analysis" echo " -modelfreeinit : Use a 'model free' analysis as initialization for the VM" echo "" @@ -236,8 +237,8 @@ if [ -z $modelfree ]; then cd "$stdir" mkdir $outdir/vm imcp $tempdir/vm/mean_cbf $outdir/vm/rcbf - fslmaths $tempdir/vm/mean_transitm -exp -mas $tempdir/mask $outdir/vm/mtt - fslmaths $tempdir/vm/mean_lambda -exp -mas $tempdir/mask $outdir/vm/lambda + fslmaths $tempdir/vm/mean_transitm -mas $tempdir/mask $outdir/vm/mtt + fslmaths $tempdir/vm/mean_lambda -mas $tempdir/mask $outdir/vm/lambda cd $tempdir # --- [ VM plus MV ] --- @@ -273,8 +274,8 @@ if [ -z $modelfree ]; then cd "$stdir" mkdir $outdir/vm_mv fslmaths $tempdir/vm_mv/mean_cbf -thr 0 $outdir/vm_mv/rcbf - fslmaths $tempdir/vm_mv/mean_transitm -exp -mas $tempdir/mask $outdir/vm_mv/mtt - fslmaths $tempdir/vm_mv/mean_lambda -exp -mas $tempdir/mask $outdir/vm_mv/lambda + fslmaths $tempdir/vm_mv/mean_transitm -mas $tempdir/mask $outdir/vm_mv/mtt + fslmaths $tempdir/vm_mv/mean_lambda -mas $tempdir/mask $outdir/vm_mv/lambda fslmaths $tempdir/vm_mv/mean_abv -thr 0 $outdir/vm_mv/rabv cd $tempdir fi