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
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Associate Professor, Institute of Biomedical Engineering, University of Oxford.
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Director of Training, EPSRC-MRC CDT in Biomedical Imaging
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Governing Body Fellow, Wolfson College, Oxford.
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