GannetLoad difficulties for version 3.5.4

MRS Software Gannet
1

Hello!

I wanted to run my 7T MEGA-sLASER twix data through the newest version of Gannet (3.5.4). I had previously used 3.3.2 and GannetLoad worked completely fine on all the files. But this time I get this error for about a third of the files:

Loading MrSpec_MRS_105_wsup.dat...
Warning: ********** An error occured while loading dataset:
'/Volumes/ExternalSSD/MRS_neuromelanin_study/Gannet/Gannet_data/MrSpec_MRS_105_wsup.dat'. Check data. Skipping to next dataset in batch.
********** 
> In GannetLoad (line 861)
In MSLASER_batch_quantification_script (line 109)

The error is identical for each failed load. Line 109 of my batch script is MRS = GannetLoad(metab, water);

The same problem arises for version 3.5.4 and 3.5.0, but not for 3.3.2. I have tried changing the on/off order in GannetPreInitialise, because that seemed work for people in the past, but it doesn’t change anything here. I’ve also made sure previous versions of Gannet are not available in the MATLAB path. I’m using the 2026a version of MATLAB on Mac Silicon, if that’s relevant/helpful!

I’d appreciate any suggestions or advice! Thank you so much :slight_smile:

2

Hi @asylvester,

Could you share the error shown in the pop-up window?

Mark

3

Hi Mark, thank you for your quick response! I’m not sure what pop-up you’re referring to… I only have the error in the MATLAB command window.

Screenshot 2026-08-14 at 15.54.50
Screenshot 2026-08-14 at 15.54.501436×507 80.4 KB

4

There should be a pop-up window that looks like this:

Screenshot 2026-08-14 at 10.26.50
Screenshot 2026-08-14 at 10.26.501006×646 108 KB

You might need to not have MATLAB in full-screen mode if you’re using a Mac with a newer OS version.

Otherwise, could you send me the GannetLoad PDFs for those datasets when you run them v3.3.2?

5

I ran it again not in full-screen, still no error report pop-up… I don’t know if MATLAB or my OS are blocking it somehow?

I’ve attached the GannetLoad from 3.3.2 for the first few problematic files.

MrSpec_MRS_105_wsup_vox1_load.pdf (523.8 KB)
MrSpec_MRS_108_wsup_vox1_load.pdf (580.4 KB)
MrSpec_MRS_109_wsup_vox1_load.pdf (530.0 KB)

6

Hmm… Could you share the Load PDFs for different datasets than run fine using both v3.3.2 and v3.5.4?

7

This is one of the working datasets in 3.3.2 and 3.5.4.

MrSpec_MRS_112_wsup_vox1_load.pdf (549.6 KB)
MrSpec_MRS_112_wsup_vox1_load.pdf (169.7 KB)

8

I have the error reports now! They didn’t come up until I let the whole batch run.

Screenshot 2026-08-14 at 17.06.44
Screenshot 2026-08-14 at 17.06.44511×249 63.3 KB

I have also now noticed that the TR is coming up as 7500ms for these files in the 3.3.2 outputs compared to 5000ms for the ones that worked… 5000ms is what I expected it to be, so I’m not sure if 7500 is a header read mistake or an acquisition mistake (but I can’t see how that could have happened - they should all be the same sequence)

1 Like
9

Yes, the pop-ups won’t appear until the end of the batch. But glad they do pop up!

I think I’ve added a fix for the error. Please update your copy of Gannet and let me know if the problem is resolved.

To clarify: The 5000 ms TR is now being shown correctly for all datasets (that you could run) when using v3.5.4?

Btw, what version of MATLAB are you running the data on at the moment? I noticed a colormap difference in the 3.5.4 Load output that only would happen if you’re using an older version of MATLAB (I think).

10

Hi Mark,

Thanks so much for working on this! It loads properly now and all of the steps work.

The TR still reads 7500ms for the ones that didn’t work the first time around, but I’ll ask our spectroscopist about that.

Re the colourmap, the 3.3.2 ones were run in MATLAB 2024a and the 3.5.4 in 2026a, so that’s why :slight_smile:

1 Like
11

Yes, I would double check with your MR tech. It’s possible that they had to increase TR because of system-dependent constraints that day on the 7T.