Dear Dr Michael your detailed responses are highly appreciated!! Thank you so much! Kindly, I have one additional question and I appreciate the response as well!
Regarding calibration using the flag -c in the command oxford_asl: I don't have proton density image and I am not sure what is the meaning of mean control image? Can I feed M0 (two columes merged together) to this flag?
When I feed M0 to the flag -c in the command oxford_asl. I get perfusion_calib.nii.gz images and the range of CBF in these images is ~150-250 while in the perfusion.nii.gz images, the CBF range is ~15-30. Are these ranges correct? Notably, when I don't include flag -c in oxford_als the range of CBF in the perfusion.nii.gz images is ~40-90 which is close to real CBF?
I have three questions regarding oxford_asl which i am using to process pcasl data
1. Can I use eddy current correct on pcasl data to correct for motion
This is not for ASL, but specifically for diffusion data. You would be better doing standard motion correction and distorition correction as appropriate.
2. Are the final CBF maps (perfusion_calib.nii.gz) represent an absolute cbf within each voxel. If so, can I normalize these images to whole brain mean using fslmaths and the flag -inm 1 to get the % of cbf within each voxel freom whole brain cbf
perfusion_calib should be in ml/100g/min and represent absolute CBF. YOu could then normalise these (and in fact oxford_asl can do that for you), rather than whole brain I would probably recommend using a grey matter ROI (the approach that oxford_asl does when doing normalisation).
3. Are the images (perfusion_calib.nii.gz) smoothed during prepossessing using oxford_asl. If not are there any recommendations for smoothing threshold. e.g. FWHM=6?
If you use the --spatial option then there is automated (data-driven) spatial regularisation applied. However, if you are then proceeding to group analysis you might want to do some spatial smoothing as is conventional in BOLD analysis (and for the same reasons, with the same tradeoff in spatial localisation vs. SNR).
Thanks
John
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Michael Chappell MEng DPhil
W: http://www.ibme.ox.ac.uk/qubic
T: +44 1865 617657
Associate Professor, Institute of Biomedical Engineering, University of Oxford.
http://www.ibme.ox.ac.uk
Director of Training, EPSRC-MRC CDT in Biomedical Imaging
http://www.onbicdt.ox.ac.uk
Governing Body Fellow, Wolfson College, Oxford.
http://www.wolfson.ox.ac.uk
PhysiologyforEngineers.org
NeuroimagingPrimers.org
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