Skip to content

Jack bsupp #20

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
jackt3 wants to merge 3 commits into
base: master
Choose a base branch
from
Open

Jack bsupp #20

Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
df25dde
Add options to adjust inversion efficiency if background suppression …
jackt3 Oct 6, 2021
47b69fc
Bug fix Log statement
jackt3 Oct 6, 2021
efc73ae
Merge branch 'master' into jack_bsupp
jackt3 Oct 6, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
26 changes: 25 additions & 1 deletion oxford_asl.in
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -155,7 +155,11 @@ Usage_extended() {
echo " User supplied PV estimates (--pvgm, --pvwm)"
echo " --pvgm : Partial volume estimates for GM"
echo " --pvwm : Partial volume estimates for WM"

echo ""
echo "Background suppression"
echo " --nbsupp=<val> : Number of background suppression inversion pulses (default 0)"
echo " --bsupp-eff=<val> : Efficiency of the background suppression pulses (default 0.95)"
echo ""
echo " Epochs "
echo " --elen : Length of each epoch in TIs"
echo " --eol : Overlap of each epoch in TIs- {deafult: 0}"
Expand Down Expand Up @@ -943,6 +947,12 @@ takeargs=0;boolarg="";isbool="";
--fast) fast=2 #do a one step analysis (NB generally a good idea to have spatial on for this option)
;;

# background suppression related arguments
--nbsupp) nbsupp=$argument
takeargs=1;;
--bsupp-eff) bsuppeff=$argument
takeargs=1;;

# fieldmap/distorition correction related arguments
--fmap) fmap=$argument
takeargs=1;;
Expand Down Expand Up @@ -2304,6 +2314,20 @@ if [ -z $alpha ]; then
fi
fi

# Adjust alpha to account for the efficiency of background suppression pulses
# if appropriate, defaulting to an assumed pulse efficiency of 0.95 if
# --bsupp-eff wasn't provided as an argument
if [ ! -z $nbsupp ]; then
if [ -z $bsuppeff ]; then
bsuppeff=0.95
fi
Log "Background suppression has been applied: $nbsupp pulses each with efficiency of $bsuppeff"
bsuppalpha=`echo "scale=10; $bsuppeff^$nbsupp" | bc`
Log "Combined background suppression pulse efficiency: $bsuppalpha"
alpha=`echo "scale=10; $alpha*$bsuppalpha" | bc`
Log "Adjusting inversion efficiency (--alpha) to account for effect of background suppression pulses: $alpha"
fi

if [ -z $cmethod ]; then
# default calibration method is 'voxelwise' unless we have CSF PV estimates or CSF mask has been supplied
if [ ! -z $fasthasrun ] || [ ! -z $csf ]; then
Expand Down