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Hi Rune, The results you see in your analysis of the data from the ASL primer website look fine to me. I would not worry that the partial volume corrected CBF value from the 10% threshold mask, as this will still contain a lot of voxels with very low proportions of white matter meaning the uncertainties on the grey matter CBF estimates are very high. To obtain the mean perfusion value in the /native_space/pvcorr/perfusion_calib_gm_mean.txt file oxford_asl masks the grey matter partial volume map at 80%. What are the values in /native_space/pvcorr/perfusion_calib_gm_mean.txt for your patient datasets? If they still seem high would you be willing to share one of your datasets with me so that I could have look? All the best, Flora Flora Kennedy McConnell ------------------------------ Postdoctoral Research Associate Institute of Biomedical Engineering<http://www.ibme.ox.ac.uk/> Department of Engineering Science University of Oxford Old Road Campus Research Building Oxford, UK OX3 7DQ ________________________________ From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Rune Monzel <[log in to unmask]> Sent: 21 September 2018 17:00:07 To: [log in to unmask] Subject: Re: [FSL] PVC with fsl_anat and oxford_asl for single TI PCASL dataset 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 '-------------------------------------------' ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1