Unable to import neuromag raw file (.fif)

lyngen · May 28, 2020, 10:32am

Hello,

Recently, I got an error message when I tried to import fif files. I also tested with the fif files which can be imported successfully last year, but Brainstorm showed me the same error message.

Here is the error message:

BST> Error: Could not find measurement data:
Unrecognized function or variable 'desc'.

99 coil definition templates available
0 MEG coil definitions and 0 EEG electrodes set up

** Error: Line 131: Reference to non-existent field 'meas_date'.
**
** Call stack:
** >in_fopen_fif.m at 131
** >in_fopen.m at 68
** >import_raw.m at 126
** >bst_call.m at 28
** >tree_callbacks.m>@(h,ev)bst_call(@import_raw,[],[],iSubject) at 636
**

It seems that the structure "meas_info" in fiff_read_meas_info.m does not provide enough information. for several variables like "dev_head_t" and "nchan".

Did I do anything wrong? How to import or review the fif file in Brainstorm?

Thanks!

Ling

Francois · May 28, 2020, 3:41pm

Hi Ling,

First make sure you don't have anything saved in your Matlab path that does not belong to the Matlab installation itself. Having other toolboxes that shadow some basic Matlab functions is a common source of problems.

BST> Error: Could not find measurement data:
Unrecognized function or variable 'desc'.

This error is generated here:

github.com

brainstorm-tools/brainstorm3/blob/master/toolbox/io/in_fopen_fif.m#L62


      
              end
          end
          
          %% ===== OPEN FIF FILE =====
          % Open file
          [ fid, tree ] = fiff_open(DataFile);
          if (fid < 0)
              error(['Cannot open FIFF file : "' DataFile '"']);
          end
          % Read info structure
          try
              [ info, meas ] = fiff_read_meas_info(fid, tree);
          catch
              err = lasterror;
              disp([10 'BST> Error: Could not find measurement data: ' 10 err.message 10]);
              info.chs = [];
              info.dig = fif_read_headpoints(fid, tree);
              meas = [];
          end
          
          % Check if file was opened successfully

This is related with an error generated in function brainstorm3/external/mne/matlab/fiff_read_meas_info.m, which is part of the external MNE-matlab library, which is maintained by a different group of developers.

There is most likely some error or unexpected data in you .fif file.
If you want help with this issue, please:

create a new issue on the mne-matlab github repository:
Issues · mne-tools/mne-matlab · GitHub
in this new issue, include a link to download you faulty .fif file
post here the link to the github issue, so that we can follow the updates

** Error: Line 131: Reference to non-existent field 'meas_date'.
**
** Call stack:
** >in_fopen_fif.m at 131
** >in_fopen.m at 68
** >import_raw.m at 126
** >bst_call.m at 28
** >tree_callbacks.m>@(h,ev)bst_call(@import_raw,,,iSubject) at 636

I posted a fix for this issue:

Update Brainstorm and try again. It will not make your data readable, but will crash in a different, hopefully slightly more elegant, way.

lyngen · June 2, 2020, 7:24am

Hi Francois,

Thank you very much for your quick response. I reported this issue to the github of MNE-matlab today.

github.com/mne-tools/mne-matlab

Unable to load raw fif file

opened 07:18AM - 02 Jun 20 UTC

closed 12:10PM - 02 Jun 20 UTC

Hui-Ling

Hi MNE-matlab team, Thanks for providing us this useful tools! Recently I… tried to read fif raw file via Brainstorm and got some error messages (as shown below). The message may indicate that the function in MNE-matlab "fiff_read_meas_info" called by in_fopen_fif.m may not read all required information from my fif files. Also, I got the same error message when I tried to read those fif files that I have ever successfully imported 6 month ago. ** Error: Line 131: Reference to non-existent field 'meas_date'. ** ** Call stack: ** >in_fopen_fif.m at 131 ** >in_fopen.m at 68 ** >import_raw.m at 126 ** >bst_call.m at 28 ** >tree_callbacks.m>@(h,ev)bst_call(@import_raw,[],[],iSubject) at 636 The following link can download a emptyroom fif file that was recorded. (Sorry. Because of the privacy issue, I could only provide the emptyroom data.) https://drive.google.com/file/d/13MmoEk58t87w85_3PPF4-Hy_AeWL1gLa/view?usp=sharing Could you please help me to figure out whether I did anything wrong? Thank you very much! Best, Ling

I reinstalled the Brainstorm that I downloaded last September. Using this old version, I can successfully import fif files and do analysis. Hope that bug will be fixed soon!

Thanks again for your help.

Best,
Ling

Francois · June 2, 2020, 10:22am

Oooops, this was the result of a bug introduced in April only in Brainstorm... the only function of MNE-matlab that is modified in Brainstorm and not reported to the MNE repo.
Sorry about that...

It's fixed: https://github.com/brainstorm-tools/brainstorm3/commit/42bcca478305bd4a15d40b8a3fa3d1c872f2b5b0
Update Brainstorm and try again.

lyngen · June 6, 2020, 11:22am

Hi Francois,

Thank you very much for your timely help!!

Ling