ON_OFF_order error after updating to Gannet 3.4 with CMRR MEGA-sLASER data

MRS Software Gannet
1

Hello all,

I’ve been trying to analyze some data collected on a 3T Siemens scanner using the CMRR MEGA-sLASER (eja) sequence. After updating from Gannet 3.3.2 to 3.4, the MRS data loaded fine in the older version, but now- after updating and adapting the initialise file, I just can’t get it to run.

I get error messages (see below) regarding the edit_on_off / ON_OFF_order settings, and changing them from the default in the initialise script also didn’t help.

I’d appreciate any guidance on how to set the edit on/off (ON_OFF_order) in Gannet 3.4 so this will run again.

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Warning: ********** An error occured while loading dataset:
‘C:\X\meas_MID00162_FID164809_pre_MEGA_sLASER_GABA.DAT’. Check data. Skipping to next dataset in batch.

In GannetLoad (line 747)
In Gannet_Batch_Script_MRS_Pilots_single (line 20)
Warning: Error updating Text.

String scalar or character vector must have valid interpreter syntax:
\fontsize{13}Filename:
C:\X\meas_MID00162\
_FID164809_pre_MEGA_sLASER_GABA.DAT

Unrecognized field name “ON_OFF_order”.

Error in SpecifyOnOffOrder (line 20)
if ~isempty(MRS_struct.p.ON_OFF_order)

Error in GannetLoad (line 330)
MRS_struct = SpecifyOnOffOrder(MRS_struct);

Error in Gannet_Batch_Script_MRS_Pilots_single (line 20)
MRS = GannetLoad(metab, water);

In defaulterrorcallback (line 12)
In msgbox (line 295)
In errordlg (line 63)
In GannetLoad (line 758)
In Gannet_Batch_Script_MRS_Pilots_single (line 20)
Warning: An error occurred while drawing the scene: Zero length string passed to TextLayout constructor.
java.lang.IllegalArgumentException: Zero length string passed to TextLayout constructor.

2

Hi @Thomas,

What is set for MRS_struct.p.ON_OFF_order in GannetPreInitialise.m?

Mark

3

Hi @mmikel!
Thanks for your help!

In my Gannetpreinitialise.m, MRS_struct.p.ON_OFF_order is set to empty ():

MRS_struct.p.ON_OFF_order = ;

I also tried it with ‘onfirst’ but I still get the same error: Unrecognized field name "ON_OFF_order".

In the old Gannetpreinitialise.m this field doesn’t exist, and when I revert to the older Gannet version the files load without issues.

4

Is it possible that the old and new Gannet versions are getting mixed up? Are the versions saved in different directories and is MATLAB using the correct GannetPreInitialise.m?

5

Thanks! I don’t think there’s a path conflict, but I’ll double-check and report back. The two versions live in separate directories and I’ve only added the one I’m using to the MATLAB path (with the corresponding Gannetpreinitialise.m).

To be safe, I’ll remove the old version completely and do a clean install of 3.4.

6

Thanks again for your help!

I ended up reinstalling Gannet, which alone didn’t fix the issue, but then I discovered that MATLAB was still using an older Gannetpreinitialise.m file that wasn’t even in the path. It was somehow shadowing the correct version from the new Gannet 3.4 folder.

After deleting the old file completely, everything now works perfectly.

If you run into similar issues, it’s worth checking for shadowed files using:

which -all Gannetpreinitialise
1 Like
7

Great! Glad to hear it’s working now.

And thanks for the heads-up about the shadowing issue!

1 Like