t1im option?

[msstringer]

Hello,

I believe Michael Chappell mentioned in his ISMRM talk that T1 maps could be used in oxford_asl. Looking through the documentation I noticed that the t1im option is mentioned, but seems to be commented out and not included in basil_options.txt. When I uncomment and run with fwdmodel_asl_rest the log file indicates that the --t1im options are unused, though Basil does set them up correctly. Do any of the supplied models allow this functionality? Sorry if I am missing something obvious, and thanks in advance if you can shed some light on this.

[mcraig-ibme]

Hi, noticed that this had been closed - it it now OK for you or is it still and issue?

[mcraig-ibme]

I'm re-opening this (having transferred it incorrectly!) because I think the issue is that --infert1 must also be specified in order to use a T1 image map in oxford_asl. However this, clearly, also allows T1 to vary which you may not want. So really what should happen is:

--t1im fixes the T1 image at ground truth
--t1im --infert1 Uses the T1 image as a prior but allows it to very
--infert1 Allows the T1 to vary using a fixed prior

The second and third of these work, but not the first.

[msstringer]

Thanks very much. I thought I had just missed the --infert1 flag (analogous to the switch being required for batim) but as you point out the behaviour differs slightly. I ran a few cases over the weekend, and there were generally very marginal changes to mean_T_1 when using --infert1, the pvcorr stage also generates a mean_T_1wm map based on the --t1 flag - 0.2.