Thank you all for the responses. For the time being I've chosen to work with my MNE preprocessed data.
Rik,
Thanks for the heads up on issues re:sensor level stats with gradiometer RMS values for unbalanced trial numbers. In all honesty, I have no other options with this dataset. We are still acquiring and there is always going to be unequal trial numbers between conditions. This is just a first pass at available data, ultimately I will be using an inversion taking into account the 'effective number of averages'.
For now, I am still figuring my way out through the SPM pipeline in sensor space. On the imaging wiki, it seems most, if not all available matlab demos use SPM5, specifically the SVL version tailored at CBU. So I've fallen back to SPM5. I've managed to convert my original datasets to SPM (*.mat,*.dat) after filtering (1-25Hz) and downsampling (666.67Hz); the resulting file size for my SPM data is 37Kb. However, when I run spm_eeg_splitFIF (GUI and/or script) on the SPM file I get an OUT OF MEMORY error in MATLAB.
Note that the spm function is part of the CBU SVL version of SPM 5; and put to use by Olaf and Jason in their MATLAB scripts on the MEG wiki. I reckon I am doing something wrong here, but not sure what! Have you encountered this problem? If not might you have any ideas what I might be doing wrong.
FYI here is the snippet of MATLAB code adapted from Olaf's (http://imaging.mrc-cbu.cam.ac.uk/meg/SensorStats). I am using a 64bit linux machine with RHEL5, and 3936840 Kb of Free Memory.
% CONVERT FROM FIFF TO SPM FORMAT (for between-condition contrasts)...
S.Fchannels = 'FIF306_setup.mat';
S.dig_method = 1; % new digitising conventions
S.conds = c; % conditions in fiff-file, MAY NEED EDITING
S.grms = 1; % so that the splitting outputs mags, grads and grad RMS (grms)
S.trig_chan = 'STI101';
S.twin = [0 Inf];
[fiffpath,fiffname,fiffext] = fileparts(fiff_files{ff});
S.Fdata = fullfile(fiff_files{ff}); % Input Fiff-file before splitting
fileSPMout = fullfile(fiffpath, [fiffname '_SPM.mat']); % Output SPM file (if not specified, will be 'myexp.mat')
S.Pout = fileSPMout; % output for conversion from Fiff to SPM format (before splitting)
D0 = spm_eeg_rdata_FIF(S); % convert fiff- to SPM-format
% SPLIT DATA INTO MAGS/GRADS/EEG...
S.D = fileSPMout; % structure for splitting
D1 = spm_eeg_splitFIF(S); % split SPM files
Best regards
Kambiz
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