You could do your own BET of the ASL data and then use that to generate the mask to pass to oxford_asl. If you use a more liberal mask you will find that the result looks more ‘messy’ as there will potentially be residual signal outside of the brain that generates contrast in the perfusion image. You are right that the mask needs to be in the native space of the ASL data. If you want to define your mask in structural space then you will need the transformation from asl to structural, inverted, to transform your mask using flirt.
My experience tends to be that ASL data doesn’t always come with the TR value set correctly in the Nifti file to begin with. However, whether this is set or not this value isn’t preserved in the output of oxford_asl, at least in part because the TR isn’t specifically relevant to the final perfusion image. Thus what you are seeing there is fine.
Michael
On 9 Oct 2017, at 14:12, Safal Khanal <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Thanks Michael. Sorry that should have been -div 0.85. And yes, the gain is 10.
I did go through the route of not passing any structural image to oxford_asl. It looked a bit messy around the skull. When you say supplying own mask, are you suggesting drawing a manual mask with fsleyes?
I believe that the mask for oxford_asl should be in ASL space. I am inclined to run bet with a lower threshold (say 0.1), and then pass this mask to oxford_asl. Does this sound sensible thing to do? Any suggestion on how I can transform the mask thus created to ASL space?
Although, it seems like oxford_asl is running fine, I am a bit surprised it is displaying incorrect TR value (1 instead of 4) while still correctly displaying the voxel sizes (picture attached).
Thanks,
Safal
On Tue, Oct 10, 2017 at 1:39 AM, Michael Chappell <[log in to unmask]<mailto:[log in to unmask]>> wrote:
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]<mailto:[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
W: http://www.ibme.ox.ac.uk/qubic
T: +44 1865 617657<tel:+44%201865%20617657>
Associate Professor, Institute of Biomedical Engineering, University of Oxford.
http://www.ibme.ox.ac.uk<http://www.ibme.ox.ac.uk/>
Director of Training, EPSRC-MRC CDT in Biomedical Imaging
http://www.onbicdt.ox.ac.uk<http://www.onbicdt.ox.ac.uk/>
Governing Body Fellow, Wolfson College, Oxford.
http://www.wolfson.ox.ac.uk<http://www.wolfson.ox.ac.uk/>
PhysiologyforEngineers.org<http://physiologyforengineers.org/>
NeuroimagingPrimers.org<http://neuroimagingprimers.org/>
<Screen Shot .png>
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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<http://PhysiologyforEngineers.org>
NeuroimagingPrimers.org<http://NeuroimagingPrimers.org>
