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
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