Hi Flora,
I tried my analysis on 2 other healthy subjects with same results/problems.
Here are 2 screenshots of the same subject using different LUT (0to120 and 100to200):
https://www.dropbox.com/s/9104h2swfmezg43/masked_pvcorr_GM_CBF_0_120.PNG?dl=0
https://www.dropbox.com/s/wt44cet3ufg6vru/masked_pvcorr_GM_CBF_100_200.PNG?dl=0
Also, I tried the analysis with a single PCASL dataset (https://users.fmrib.ox.ac.uk/~chappell/asl_primer/ex2/index.html) using the code at the bottom. The results are just a litte bit too high:
Masked (90% PV GM threshold) CBF GM mean±std: 50.72±18.93
Masked (10% PV GM threshold) CBF GM mean±std: 45.38±22.25
Masked (90% threshold) partial volume corrected CBF GM mean±std: 57.97±22.09
Masked (10% threshold) partial volume corrected CBF GM mean±std: 85.96±46.22
Do you think this is reasonable?
Thank you for your help.
Regards,
Rune
fsl_anat -i singlePLDpcASL/T1.nii.gz
echo 'done with fsl_anat'
echo '-------------------------------------------'
# using oxford_asl version v3.9.15 Mon Jul 9 15:31:19 2018
~/Downloads/oxford_asl/oxford_asl -i singlePLDpcASL/asltc.nii.gz -o oxasl --bat=0 --casl --iaf=tc --tis=3.6 --bolus=1.8 --slicedt=0.0452 --spatial --mc \
-c singlePLDpcASL/aslcalib --tr 4.8 --cblip=singlePLDpcASL/aslcalib_PA --pedir=y --echospacing=0.06 --fslanat=singlePLDpcASL/T1.anat --pvcorr
echo 'done with oxford_asl example'
echo '-------------------------------------------'
# folder names
aslFolder=oxasl
~/Downloads/oxford_asl/oxford_asl -i singlePLDpcASL/asltc -o $aslFolder \
--wp \
--spatial=off \
--casl \
--iaf=tc \
--tis=3.6 \
--bolus=1.8 \
--slicedt=0.0452 \
--mc \
-c singlePLDpcASL/aslcalib.nii.gz \
--tr 4.8 \
--cblip=singlePLDpcASL/aslcalib_PA.nii.gz \
--pedir=y \
--echospacing=0.06 \
--fslanat=singlePLDpcASL/T1.anat \
--pvcorr
echo 'done with own oxford_asl code'
echo '-------------------------------------------'
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