OspreyLoad error when trying to load TWIX files from Connectom

Dear Osprey Developers,

I hope you are well!

I’ve come across an issue when using OspreyLoad to load TWIX files, both in the command line and in the GUI, and I was hoping you might be able to help me. Our data is from a Siemens Connectom scanner so this could have something to do with it. I tried viewing the .dat file in MATLAB and it looked different to the .dat files from the TWIX example data provided with Osprey - not sure if this is related.

The error message I get is:

>> Osprey
Timestamp March 09, 2022 13:05:43 Osprey 1.1.0  OspreyGUI
Warning: "/cubric/software/spm.versions/spm12/external/fieldtrip/external/stats/finv.m" not found in path. 
> In rmpath (line 71)
In osp_Toolbox_Check (line 84)
In Osprey (line 19) 
Warning: MATLAB has disabled some advanced graphics rendering features by switching to software OpenGL. For more information,
click here. 
Continue with loading new job, overwriting existing job.
/home/sapcm15/gitlab/ALSPAC_analysis/MRS/jobTwix_ALSPAC.m
Timestamp March 09, 2022 13:07:26 Osprey 1.1.0
Timestamp March 09, 2022 13:07:27 Osprey 1.1.0  OspreyGUI
Timestamp March 09, 2022 13:07:51 Osprey 1.1.0  OspreyLoad
Loading raw data from dataset   1 out of   1 total datasets...
Software version: VD (!?)
Reader version: 1496740353 (UTC: 06-Jun-2017 09:12:33)
Scan 1/1, read all mdhs:
    65.8 MB read in    1 s

ans =

     0

single RAID file detected.
Software version: VD (!?)
Reader version: 1496740353 (UTC: 06-Jun-2017 09:12:33)
Scan 1/1, read all mdhs:
     4.7 MB read in    0 s

ans =

     0

single RAID file detected.

... done.
 Elapsed time 4.856217 seconds
Array indices must be positive integers or logical values.

Error in OspreyLoad (line 168)
            for pp = 1:raw.sz(raw.dims.extras)

Error in osp_onLoad (line 33)
    MRSCont = OspreyLoad(MRSCont);
 
Error while evaluating UIControl Callback.

Please let me know if there is anything you need from me.

Thank you so much,
Carolyn

Hi @CarolynMcNabb,

Thanks for reaching out.

It is quite possible that the automated loader is not recognizing this specific sequence (and how the averages etc. are stored in the twix file), as you have already mentioned. This will result in some miss-matched entries in MRS container and the subsequent crash.

This is usually an easy fix in the code. Could you supply me (hzoelln2@jhmi.edu) the data? Also is this conventional or edited data?

Best,
Helge

Hi @Helge,

Thank you so much for your response. The data are conventional data (PRESS sequence). I have shared a OneDrive folder containing the water suppressed and water unsuppressed data with you but please let me know if you need anything else.

Thanks again!
Carolyn

Hi @CarolynMcNabb,

I have just uploaded a bug fix to the develop branch which solves the issues with the test data you have supplied me. Let me know if this works for you.

It is possible that this solution is not working for other sequence you may acquire on the Connectom scanner (i.e. MEGA-PRESS).

Best,
Helge

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Thank you so much, @Helge! It worked like a charm!!

Have a wonderful weekend.

Best wishes,
Carolyn

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