Thanks, that's really helpful - I now have perfusion in the right bits of the brain!
I do think it could be improved though as I have collected fieldmaps, though that I don't *think* I am currently benefiting from them. Prior to finding these great tools, I had a long pathway of registration:
1. Mzero(calibration image) to raw ASL (partial FOV) using flirt
2. ASL data to wholehead ASL using flirt
3. Wholehead to highres structural using bbr with fieldmaps
4. highres to standard using flirt
I then concatenated the mat files and reversed it to create an ASL2Standard.mat file. This is what I used to transform the perfusion_calib map from the asl_gui results. Will this apply the advantages of B0 unwarping from the bbr stage to the perfusion map, if not directly done on the perfusion_calib map? Or is it not that simple?!
I guess I am uncertain exactly what to input into the oxford_asl or gui to ensure its as good a result as I can get.
thanks in advance,
Ella
Previous message:
Ella,
Those warnings are not a concern they relate to the size of the databased and that some internal variables will not be saved - but you wouldn't need these.
You can still use a low res structural with oxford_asl - you should find that asl_gui will run an oxford_asl command that you can copy and reuse adding the -r option to load in the low res structural data (make sure that this has been BETed). Otherwise you can play with asl_reg. The general recommendation is to register your raw asl data (before tag control subtraction) to the structural and then apply the transformation from that to your (native_space) perfusion image that comes out of the analysis. It is always best to do the actual perfusion quantification with the original data. You might try registration with the perfusion image directly, my experience is that this is less reliable, but you might give it a try.
Michael
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