Step 2 of 3: VB - Tissue Arterial - Initialise with step 1 Using fabber - Taking too much time

[ampaschoal]

Hi all,

I was using the oxasl with FSL version 6.0.1 and it was running well. Last week I updated my FSL to 6.0.4 and when using oxasl (or oxford_asl), the Step 2 of BASIL analysis is taking too much time, so much that I cant finish (one hour for 1%). Here is the print of my try. I am using Ubuntu 18.04.

Did it happen with anybody else? What should I do to solve it?

I already tried to re-install my FSL as well as the oxasl.

[ampaschoal]

After installing back the 6.0.1 version of FSL, I could run again the oxasl.

[mcraig-ibme]

Sorry for the slow response, I have not been getting Github notifications on this repository. I am not aware of any problems with Fabber in FSL 6.0.4. Was the first step (which seems to have completed) also very slow, or did that finish in reasonable time?

[ampaschoal]

No, the first step was quick. The second step I couldn't finish. I waited for a few hours and it still was at the beginning. I have no clue why. But after installing back an older version of FSL it worked, so I didn't try again on version 6.0.4.

[mcraig-ibme]

My best guess is that there was a numerical instability in the model. This can cause Fabber to fill up its logfile with huge amounts of data which would certainly slow it down a lot. If you have a data sample that you are able to share then I might be able to investigate and reproduce it. The issue definitely looks to be in fabber itself which would fit with the change in behaviour on installing a different version of FSL.

[robbwh]

I similarly can only get the arterial inference to work (within a reasonable timeframe) when using FSL 6.0.1.

Using FSL 6.0.5.1 it runs so slowly that I doubt it would complete within 24 hours.

The reason for this is unclear to me. Using the fmrib example multi-pld data, oxasl/oxford_asl run will complete just fine regardless of version.

I am unable to share data currently, but the data come from a test subject acquired using the ADNI4 multi-pld pCASL scan card.

EDIT:
if --bat=1.3 (which is default for pCASL, will not run). If bat is specified lower, like --bat=0.7 to --bat=1.25, it will run