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
On 22 Jan 2014, at 14:06, Ella Hinton <[log in to unmask]> wrote:
> Hi
> Thanks for your email. That's cracked it - running the same analysis without the 'Incorporate T1 value uncertainty' option lead to no fatal errors, thankfully! Possibly a bug then as you suggest?
>
> I did still get the same warnings as before though - should I be concerned with those?!
>
> Finally, I should note that the registration part hasn't worked at all. I have a small field of view for the asl data (pASL), which isn't registered the structural at all well. I do have a low res wholehead scan to incorporate, so I will try asl_reg next (as the old option to include it in the gui is no longer there?). Please forgive the next dumb question, but should I register the images (ASL data, wholehead scan, structural) first before entering them into Asl gui, or should I register the resulting perfusion map?
>
> Many thanks for your help
> Ella
>
>
> Previous message:
>
> Ella,
>
> I am glad that you have made some progress. The key error here is the 'Option doesn't begin with' issue and it sounds like there may be a bug in the GUI for one of the options you have selected - it would be useful to know more details about what options from the GUI you are using. My suggestion to start with is to try turning off 'Incorporate T1 value uncertainty' first and see if it runs and then if not, turn off 'Use adaptive spatial smoothing on CBF'. That might help us to diagnose the issue.
>
> Thanks,
> Michael
>
> On 22 Jan 2014, at 08:32, Ella Hinton <[log in to unmask]> wrote:
>
>> Hi again
>>
>> Further to my email yesterday re the Asl_gui, I then found the previous message (apologies for missing this before) and have had our FSL version updated to 5.0.6. This has solved the original problem.
>>
>> Now the script runs, but I get 'FATAL ERROR ENCOUNTERED'. I have scoured the error log file and the following summary of warnings and errors are given:
>> Summary of warnings (2 distinct warnings)
>> Issued 60 times: Cache is disabled to avoid memory problems!
>> Issued once: Not saving finalSpatialPriors.nii.gz -- too huge!!
>>
>> then further down:
>> Calculating variance for: T_1
>> FABBER: MVNtool
>> Option doesn't begin with --: 4
>>
>> An exception has been thrown
>> Runtime error:- An option doesn't begin with --
>>
>> Is this error due to the figured and options I've selected? I would be really grateful for some advice.
>>
>> thanks
>> Ella
>>
>
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