Dear Andrej,
I think the issue you mention with respect to the fiducials is a general
problem with the conversion process, as it also affects our site, which has
a 248-channel 4D system. In looking at the SPM code for reading the native
4D data, In looking at the function, it seems to me that it assumes the
fiducials will be in the headshape file. In the 4D format, they are in the
config file, however. You can always manually input them into the resulting
D structure (in the .mat file output from spm_eeg_convert.m.
As to the number of channels you have, the SPM routines automatically import
all channels in the dataset. Are you absolutely certain that only the MEG
and reference channels are in your datasets (also, by default, there may be
a Trigger channel, Response Channel and a UACurrent Channel for the coils on
head)? You can confirm this by looking at one of your datasets or at the
template file you used for acquisition. On your system, there are a number
of external inputs available (e.g., for EEG) that might be turned on (96 of
them on our system). When we import using the spm_eeg_convert function, we
get the correct number of channels on our system. Have you tried selecting
MEG only during the import? There are numerous other problems for us, but
that one is correct. The file format for the 148 and 248 channel systems is
the same, so that shouldn't be an issue.
Feel free to contact me off-list if you like. We've analyzed a lot of 4D
datasets using spm5 and now spm8. Generally we've been using our own
converters because of the difficulties we've had using the spm conversion
routines.
Best,
Don
On 1/28/09 4:14 AM, "Vladimir Litvak" <[log in to unmask]> wrote:
> Dear Andrej,
>
> The message is actually quite informative about the problem. SPM uses
> routines for reading BTi data developed by Jan-Mathijs Schoffelen from
> Glasgow. As said in the message there might be problem having to do
> with the fact that your BTi sytem is different from his. It looks like
> the conversion proceeds to the end but as you say the results are
> incorrect. SPMs messages except for Jan-Mathijs's warnings are normal
> and do not indicate a problem. I suggest that you get in touch with
> Jan-Mathijs ([log in to unmask]) and ask for his help in
> resolving the problem. Also if there are other BTi users on the list
> who can help with resolving this problem I suggest that they contact
> Jan-Mathijs with their suggestions.
>
> Best,
>
> Vladimir
>
> On Wed, Jan 28, 2009 at 10:49 AM, Andrej Stancak
> <[log in to unmask]> wrote:
>> Dear SPM experts,
>>
>> I have tried to load our 4D MEG data set, that has 148 MEG sensors and 17
>> non-MEG signals (=165), into SPM8b. After calling Convert from the GUI, I
>> get a lengthy message (below) but what is worse, the number of channels read
>> is wrong - it is 290 instead of the correct number 165. Also fiducials are
>> not read (however, they are available in the header), and other information
>> seems to be missing as well. I would be grateful for adjusting the reading
>> of MEG data for 4D-148 sensors machine, if possible.
>>
>> Best regards
>> Andrej Stancak
>>
>>
>> Here is the message I get by calling Convert in SPM8b:
>>
>> Warning: reading in weight table: no warranty that this is correct. it seems
>> to work for the
>> Glasgow 248-magnetometer system. if you have some code yourself, and/or
>> would like to test it
>> on your own data, please contact Jan-Mathijs
>>> In fileio\private\read_4d_hdr at 252
>> In fileio\private\read_header at 474
>> In fileio_read_header at 11
>> In spm_eeg_convert at 73
>> In spm_eeg_convert_ui at 81
>> Warning: reading in weight table: no warranty that this is correct. it seems
>> to work for the
>> Glasgow 248-magnetometer system. if you have some code yourself, and/or
>> would like to test it
>> on your own data, please contact Jan-Mathijs
>>> In fileio\private\read_4d_hdr at 252
>> In fileio\private\read_header at 474
>> In fileio\private\read_event at 426
>> In fileio_read_event at 11
>> In spm_eeg_convert at 95
>> In spm_eeg_convert_ui at 81
>> converting units from 'm' to 'mm'
>> Warning: reading in weight table: no warranty that this is correct. it seems
>> to work for
>> the Glasgow 248-magnetometer system. if you have some code yourself, and/or
>> would like to
>> test it on your own data, please contact Jan-Mathijs
>>> In fileio\private\read_4d_hdr at 252
>> In fileio\private\read_header at 474
>> In fileio\private\read_sens at 146
>> In fileio\private\read_headshape at 144
>> In fileio_read_headshape at 11
>> In spm_eeg_convert at 398
>> In spm_eeg_convert_ui at 81
>> Warning: Could not obtain fiducials automatically.
>>> In spm_eeg_convert at 400
>> In spm_eeg_convert_ui at 81
>> checkmeeg: no channel type, assigning default
>> checkmeeg: no units, assigning default
>> checkmeeg: transform type missing, assigning default
>> checkmeeg: data scale missing, assigning default
>> checkmeeg: data type is missing or incorrect, assigning default
>> creating layout from cfg.grad
>> creating layout for bti148 system
>>
--
Donald C. Rojas, Ph.D.
Associate Professor of Psychiatry and Neuroscience
Director, Magnetoencephalography Laboratory
University of Colorado Denver
Department of Psychiatry, Mail Stop F-546
Anschutz Medical Campus, Building 500 N2224G
13001 E 17th Place
PO Box 6508
Aurora CO 80045-0508
303-724-4994
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