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Hi Rune, I agree that your partial volume corrected perfusion values seem very high. As far as I can see, all of your analysis looks sensible. so I am not sure why you are seeing these high perfusion values. Have you had a look at the native_space/pvcorr/perfusion_calib.nii.gz image? Does it look strange at all, e.g. are there any areas with particularly high perfusion, or is it just globally brighter? Have you tried your analysis on another of your patients? If so, do you see similarly high perfusion values? Also, I was wrong about the --echospacing parameter in your analysis. When you provide a --cblip image oxford_asl uses topup to perform distortion correction (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup/TopupUsersGuide#A--datain), so the value you provide for the --echospacing parameter should actually be the total readout time (defined as the time from the centre of the first echo to the centre of the last) in seconds, so your original value was in the right range. Apologies for the confusion, this is something I will make sure is clarified in the oxford_asl help in the future. All the best, 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: 30 August 2018 17:13:21 To: [log in to unmask] Subject: Re: [FSL] PVC with fsl_anat and oxford_asl for single TI PCASL dataset Hi Flora, 1) They are both from one subject: mean+std 46+27 ml/100g/min is the normal CBF quantiziation of WM+GM mask (so whole brain). 97+56 ml/100g/min is just the GM mask. 2) yes, it is the masked grey matter perfusion image which has this high values 3) it is a result by the "--pvcorr" functionality which use the results of fsl_anat which generates the PV maps. oxford_asl returns me a mask (native_space/gm_mask.nii.gz) and also an image called "perfusion_calib_masked.nii.gz" in folder native_space/pvcorr. I used this map to calculate CBF in GM which is 97+56 ml/100g/min (mistake before, sorry, it is GM CBF!). Your further questions and answers: 1) Just checked both images in fsleyes: You are right, it is just a small re-orientation. 2) it is a whole brain mask, just to get rid of the noisy background. 3) That's a point I have to check, thank you. By looking at the distortion corrected map (which already did) I did not find any abnormalities. I used ms because of the example (https://users.fmrib.ox.ac.uk/~chappell/asl_primer/ex2/index.html), which is also has --echospacing=0.06.. but you are right, the docs in oxford_asl are saying seconds. 4) Yes, we have a strong background suppression which leads to a labeling efficiency of 0.6. Also the quantitative CBF image which I find in folder native_space/perfusion_calib.nii.gz is in the normal range (CBF (using mask WM+GM) mean+std: 46+27 ml/100g/min). The patient is a subject, yes. Also I just validated the PVC: I calculated the recombined CBF image: recCBF = pvGM * pvcorrGM_masked + pvWM * pvcorrWM_masked recCBF is with r=0.97 (alpha=0.95) very close to the normal calculated CBF image... Thank you for your help and taking your time Best, Rune ######################################################################## 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