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You can supply your own mask to oxford_asl and it will then do the quantification within that. For this case, I might be tempted to do your registration separately and just use oxford_asl to do the perfusion quantification within a mask defined on the whole head or even just the whole image volume (and thus not supply the structural image to oxford_asl at all).

For your calibration command, I think you want to divide by 0.85 (I presume this is your inversion efficiency), is the factor of 10 a difference in gain between label-control images and M0 image?

Michael


On 9 Oct 2017, at 09:12, Safal Khanal <[log in to unmask]> wrote:

Dear Michael and ASL'ers

I am having to generate a perfusion image for the whole head brain as I would like to retain most of the ocular tissues. Is there a way I can accomplish this using oxford_asl as the recommended protocol always seems to create a BETed mask automatically even if the whole head structural image is supplied and resultant perfusion image as per the extracted mask?

Also, does the following code look reasonable for calibration of the perfusion image (pcasl)?

fslmaths perfusion -div M0_reg.nii -mul 0.9 -mul 0.85 -mul 6000 -div 10 final_perfusion

Appreciate your help!

Regards,
Safal

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Michael Chappell MEng DPhil
    T: +44 1865 617657
Associate Professor, Institute of Biomedical Engineering, University of Oxford.
Director of Training, EPSRC-MRC CDT in Biomedical Imaging
Governing Body Fellow, Wolfson College, Oxford.
    http://www.wolfson.ox.ac.uk