[FieldTrip] MNE fiff_read / write_raw_segment
Peter Goodin
pgoodin at swin.edu.au
Sat Jan 26 12:42:10 CET 2013
Hi Gianpaolo (or anyone else that can help me out again),
Again, thank you very much for putting me onto mne_ex_read_write_raw.m. Unfortunately I am still having problems.
Because I appear to have been not too forthcoming in my original email, the problem is with the triggering in our neuromag triux (306 channel) system,
I'm having triggers add onto each other and others fail to register with the trigger channels. I've written a script to read in the trigger information from my stimuli presentation software and want to write the accurate data to the main trigger channel (STI101), then save as a new fiff file. By adding code from mne_ex_read_write_raw.m to my overall script (reading the entire data set into memory at once), I'm able to replace the questionable STI101 data with that obtained from my stim software, but have a problem when writing the new fiff file. The size of the input file is ~2gb but when writing, the output is approx ~18gb. I suspect I'm writing a WHOLE bunch of redundant data, but am unable to open the new file, even on a machine running 16gb RAM.
I've attached the script and would be extremely grateful for any advice that could be given.
Thanks again to everyone on the mailing list whose helped me out so far,
Peter.
_________________________
Peter Goodin,
BSc (Hons), Ph.D Candidate.
Brain and Psychological Sciences Research Centre (BPsych)
Swinburne University,
Hawthorn, Vic, 3122
Monash Alfred Psychiatry Research Centre (MAPrc)
Level 1, Old Baker Building
Commercial Road
Melbourne, Vic, 3004
________________________________
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Peter Goodin [pgoodin at swin.edu.au]
Sent: Thursday, 24 January 2013 11:05 PM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] MNE fiff_read / write_raw_segment
Hi Gianpaolo,
Wonderful! This is exactly what I'm after! Thank you very much for pointing me in the correct direction!
Peter
__________________________
Peter Goodin,
BSc (Hons), Ph.D Candidate.
Brain and Psychological Sciences Research Centre (BPsych)
Swinburne University,
Hawthorn, Vic, 3122
Monash Alfred Psychiatry Research Centre (MAPrc)
Level 1, Old Baker Building
Commercial Road
Melbourne, Vic, 3004
________________________________
From: fieldtrip-bounces at science.ru.nl [fieldtrip-bounces at science.ru.nl] on behalf of Demarchi, Gianpaolo [gianpaolo.demarchi at unitn.it]
Sent: Thursday, 24 January 2013 9:13 PM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] MNE fiff_read / write_raw_segment
Hi Peter,
for a similar purpose (i.e. cleaning the trigger lines) I found very helpful copying from an example file:
mne_ex_read_write_raw.m
which is in the mne folder as well. This is a nice example script which instructs you on how to open, write and close properly a fiff file, with all the details and parameters explained.
Basically, I just copied and pasted the relevant lines, and put some intelligence in the
%
% You can add your own miracle here
%
part (namely, changing accordingly the data(channel, time) matrix).
It's straightforward, but just post back in case of need ...
Best luck,
GP
Il giorno 24/gen/2013, alle ore 10:11, Peter Goodin <pgoodin at swin.edu.au<mailto:pgoodin at swin.edu.au>> ha scritto:
Hi Alex,
Sorry, that "add" in the first sentence is a little misleading. Please accept my apologies.
I'm trying to alter an existing channel with new values, not add a new channel. If the channel already exists but is having the data rewritten, do any changes need to be made to fh.info.ch<http://fh.info.ch> or any other aspect of fh?
Thanks and sorry for the confusion again.
Peter.
__________________________
Peter Goodin,
BSc (Hons), Ph.D Candidate.
Brain and Psychological Sciences Research Centre (BPsych)
Swinburne University,
Hawthorn, Vic, 3122
Monash Alfred Psychiatry Research Centre (MAPrc)
Level 1, Old Baker Building
Commercial Road
Melbourne, Vic, 3004
________________________________________
From: fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl> [fieldtrip-bounces at science.ru.nl<mailto:fieldtrip-bounces at science.ru.nl>] on behalf of Alexandre Gramfort [alexandre.gramfort at inria.fr<mailto:alexandre.gramfort at inria.fr>]
Sent: Thursday, 24 January 2013 5:38 PM
To: FieldTrip discussion list
Subject: Re: [FieldTrip] MNE fiff_read / write_raw_segment
hi Peter,
when you add channels to a fif structure you need to update the measurement
information (channels names, types etc.). With your notations you should update
fh.info.chs
hope this helps
Alex
On Thu, Jan 24, 2013 at 2:59 AM, Peter Goodin <pgoodin at swin.edu.au<mailto:pgoodin at swin.edu.au>> wrote:
Hi Fieldtrip list,
I'm trying to add an altered channel and save it as a new fiff file using
the MNE commands from the external/MNE dir in Fieldtrip, but seem to just
keep getting the data from the old fiff file instead.
The code I'm currently using is:
To read:
fh = fiff_setup_read_raw('input.fif');
f = fiff_read_raw_segment(fh);
After adding in the altered channel data to f, I then use:
fiff_write_raw_segment(output.fif, fh);
What I thought would happen is output.fif would use the information in f and
fh to write output.fif, but what seems to be happening is the data in f is
being ignored.
Does anyone have any ideas on how to insert the altered channel data then
write it back out as a fiff file?
Thanks,
Peter.
__________________________
Peter Goodin,
BSc (Hons), Ph.D Candidate.
Brain and Psychological Sciences Research Centre (BPsych)
Swinburne University,
Hawthorn, Vic, 3122
Monash Alfred Psychiatry Research Centre (MAPrc)
Level 1, Old Baker Building
Commercial Road
Melbourne, Vic, 3004
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--
------------------------------------------------------------------------
Gianpaolo Demarchi, PhD gianpaolo.demarchi at unitn.it<mailto:gianpaolo.demarchi at unitn.it>
MEG Lab phone: 0039 0461 28 30 76
CIMeC - Mind/Brain Center University of Trento
Via delle Regole, 101 I-38100 Mattarello di Trento (TN), Italy
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