Dear Diane,

Things are becoming clearer and I think we are quite close to
resolving your problems.

> We have a 64-channel standard Biosemi system. From what I understand, you
> can order Biosemi with 32, 64, 128, or 256 channels. Can SPM work with 64
> channels if they have standard 10-20 names?

We haven't seen a Biosemi system with less than 128 channels but since
you have one, it should be supported. The question is, is the EEG cap
you are using a standard one for 64-channel Biosemi or is it something
you ordered separately and other labs with 64-channel Biosemi systems
are likely to have other caps? Also is the mapping between Biosemi and
10-20 labels that you are using just something approximate or do you
have some documentation from Biosemi saying that this is the right
correspondence?

The reason I'm asking you all this is as follows. If your system can
be considered a standard Biosemi 64 system, then I can add default
support for it in SPM. I have already added automatic recognition of
EEG channels and to make it complete I need a file with 3D electrode
positions. If you are sure that the channels correspond exactly to
10-20 locations, then just send me the full label mapping you are
using and I'll make this file myself. If not, then perhaps you can
find somewhere a locations file with fiducials for your cap or you can
make a good quality measurement in your lab with a 3D digitizer.

If your cap is something that is not likely to come with other
Biosemi-64 systems then we still can make a locations file for you,
just it won't be included in SPM distribution. Then you won't have to
rename your channels with the GUI every time.

> Ok, this sounds good. It's strange to me that the filtering function
> requires channel names to work.

The problem here is that not all channels should be filtered. For
instance trigger channels should not. The filtering function doesn't
use channel names but it does use channel types so the types should be
set correctly before filtering.

> Is it necessary to include a negative baseline? We want to exclude the
> visually evoked potentials, which is why we are interested in 0.5 seconds to
> 4.0 seconds.
>

In principle it's not necessary but most epoched files have negative
baseline and SPM5 required it. There might still be some unfixed bugs
related to that, like the one I found in spm_eeg_filter. I think you
should continue the way you are working now and report any problems to
me.


> There is a strong VEP at 0-0.5 seconds, but we are not interested in that.
> Actually, we'd like to perform time-frequency analysis on a single-trial
> basis rather than ERP analysis. Can SPM calculate an inverse solution for
> non-averaged data?

SPM can look at induced activity based on single trials (see the
manual) but this is something that we don't yet have much experience
with. There are now several people testing this functionality and I
can put you in touch with them if you want. What is not possible is to
perform time-frequency analysis at the channel level and then
source-reconstruct the power data, because once you discard phase
information source reconstruction is not possible any more.

> Shouldn't the data be filtered prior to down-sampled? Otherwise, the effects
> of aliasing will distort the data?

No, it's OK. The downsampling function in Matlab is aware of aliasing
so it performs filtering prior to downsampling.

> One thing I'm not clear about, however,
> is whether the data should be downsampled and filtered before or after
> epoching.

It depends, but I'd say if your continuous data is not much bigger
than your epoched data (i.e. if you don't have too much dead time in
your recordings) perhaps you should downsample and filter before
epoching. That's always a safer option.


So I'd suggest the following sequence:

Convert -> Prepare (get the labels, types, channel locations etc.
right) -> Downsample -> Filter ->Epoch ->Artefact rejection->3D source
reconstruction

You don't need averaging because to look at induced activity you need
a file with single trials. You can try switching filtering and
downsampling to see if it makes any difference but I don't think it
should.

Regarding the 'Prepare' stage I need some more information about the
cap and then I'll tell you exactly what to do.

Best,

Vladimir




>>
>> >>
>> >> On Fri, Jun 19, 2009 at 11:01 AM, Diane
>> >> Whitmer<[log in to unmask]>
>> >> wrote:
>> >> > Vladimir,
>> >> > The problem of losing my data is arising at the time of filtering.
>> >> > Are the filter functions supposed to work on epoched data? If so, is
>> >> > there
>> >> > anything special I should do to get the filtering to work? e.g. I am
>> >> > trying
>> >> > to high pass above 2 Hz using the gui. My sampling rate is 2048 Hz
>> >> > and
>> >> > my
>> >> > epochs are 3.5 seconds in length.
>> >> > Thank you,
>> >> > Diane
>> >> >
>> >> >
>> >> > On Thu, Jun 18, 2009 at 1:47 PM, Vladimir Litvak
>> >> > <[log in to unmask]>
>> >> > wrote:
>> >> >>
>> >> >> Display->M/EEG
>> >> >>
>> >> >> On Thu, Jun 18, 2009 at 12:37 PM, Diane
>> >> >> Whitmer<[log in to unmask]>
>> >> >> wrote:
>> >> >> > Hi Vladimir,
>> >> >> > How do I access the Reviewing tool?
>> >> >> > When I look under Prepare > Review, I cannot find the EEG traces.
>> >> >> > Thanks,
>> >> >> > Diane
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > On Thu, Jun 18, 2009 at 12:57 PM, Vladimir Litvak
>> >> >> > <[log in to unmask]> wrote:
>> >> >> >>
>> >> >> >> Dear Diane,
>> >> >> >>
>> >> >> >> The file you sent me contains just zeros in the data so it's not
>> >> >> >> surprising that SPM can't do much with it. Also the montage you
>> >> >> >> applied is just an identity matrix so it doesn't do anything, but
>> >> >> >> that's not the reason why the data is invalid. You should use the
>> >> >> >> reviewing tool to see at which stage in the processing your data
>> >> >> >> disappears.
>> >> >> >>
>> >> >> >> Best,
>> >> >> >>
>> >> >> >> Vladimir
>> >> >> >>
>> >> >> >> On Thu, Jun 18, 2009 at 11:42 AM, Diane
>> >> >> >> Whitmer<[log in to unmask]>
>> >> >> >> wrote:
>> >> >> >> > Hi Vladimir,
>> >> >> >> > I changed the montage to average reference, and then averaged
>> >> >> >> > my
>> >> >> >> > trials.
>> >> >> >> > The same error message appears when I try to run the Inverse
>> >> >> >> > Solution.
>> >> >> >> > I just sent both the .dat and the .mat via yousendit.
>> >> >> >> > Please let me know if you are able to figure out the source of
>> >> >> >> > the
>> >> >> >> > errors. I
>> >> >> >> > *very much* appreciate your help.
>> >> >> >> > Sincerely,
>> >> >> >> > Diane
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > On Wed, Jun 17, 2009 at 12:29 PM, Vladimir Litvak
>> >> >> >> > <[log in to unmask]> wrote:
>> >> >> >> >>
>> >> >> >> >> Dear Diane,
>> >> >> >> >>
>> >> >> >> >> Your new montage is quite good, but you should decide what you
>> >> >> >> >> want
>> >> >> >> >> to
>> >> >> >> >> do about the 'EXG1' channel. Presently it appears in the
>> >> >> >> >> montage,
>> >> >> >> >> but
>> >> >> >> >> is actually set to zero. I understand this is your reference.
>> >> >> >> >> I
>> >> >> >> >> saw
>> >> >> >> >> in
>> >> >> >> >> the history that you are using SPM's default channel
>> >> >> >> >> locations.
>> >> >> >> >> SPM
>> >> >> >> >> wouldn't have a location for EXG1 and wouldn't mark it as
>> >> >> >> >> 'EEG'
>> >> >> >> >> by
>> >> >> >> >> default. So you have two options:
>> >> >> >> >>
>> >> >> >> >> 1) If you want to use it as an extra EEG channel you need to
>> >> >> >> >> either
>> >> >> >> >> change its name to some 10-20 name and assign default channel
>> >> >> >> >> types
>> >> >> >> >> and default locations again or at least change its type to
>> >> >> >> >> 'EEG'
>> >> >> >> >> in
>> >> >> >> >> the 'prepare' interface and load a locations file where this
>> >> >> >> >> channel
>> >> >> >> >> appears. Then you should make a montage like what you did just
>> >> >> >> >> with
>> >> >> >> >> 65
>> >> >> >> >> channels including EXG1 so
>> >> >> >> >> tra = eye(65) - ones(65)/65;
>> >> >> >> >>
>> >> >> >> >> 2) If you can live without it, you can use the montage you
>> >> >> >> >> sent
>> >> >> >> >> me,
>> >> >> >> >> or
>> >> >> >> >> even simpler just don't include EXG1 in the montage at all.
>> >> >> >> >> You
>> >> >> >> >> can
>> >> >> >> >> either keep it in the file as a non-EEG channel or not keep
>> >> >> >> >> it,
>> >> >> >> >> for
>> >> >> >> >> source reconstruction it doesn't matter.
>> >> >> >> >>
>> >> >> >> >> Once you convert the data to average reference, try the source
>> >> >> >> >> reconstruction again. If there is still a problem, average
>> >> >> >> >> your
>> >> >> >> >> data
>> >> >> >> >> and see if for averaged data you get the same error message.
>> >> >> >> >> If
>> >> >> >> >> so
>> >> >> >> >> send it to me, the file will be much smaller. If you only get
>> >> >> >> >> the
>> >> >> >> >> error for epoched data, but not for averaged let me know and
>> >> >> >> >> we'll
>> >> >> >> >> think of a way for you to send me the epoched file.
>> >> >> >> >>
>> >> >> >> >> Best,
>> >> >> >> >>
>> >> >> >> >> Vladimir
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >>
>> >> >> >> >> On Wed, Jun 17, 2009 at 11:12 AM, Diane
>> >> >> >> >> Whitmer<[log in to unmask]>
>> >> >> >> >> wrote:
>> >> >> >> >> > Vladimir,
>> >> >> >> >> > I tried to send the .dat file, but it was over 100MB and
>> >> >> >> >> > therefore
>> >> >> >> >> > cannot be
>> >> >> >> >> > sent via yousendit without a subscription. Do you have
>> >> >> >> >> > another
>> >> >> >> >> > suggestion?
>> >> >> >> >> > Thanks,
>> >> >> >> >> > Diane
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> > On Tue, Jun 16, 2009 at 9:38 PM, Vladimir Litvak
>> >> >> >> >> > <[log in to unmask]>
>> >> >> >> >> > wrote:
>> >> >> >> >> >>
>> >> >> >> >> >> Dear Diane,
>> >> >> >> >> >>
>> >> >> >> >> >> The error might have something to do with the fact that the
>> >> >> >> >> >> montage
>> >> >> >> >> >> matrix you used is wrong. To do what you intended you'd
>> >> >> >> >> >> need
>> >> >> >> >> >> the
>> >> >> >> >> >> transpose of what you specified, but as I mentioned to be
>> >> >> >> >> >> on
>> >> >> >> >> >> the
>> >> >> >> >> >> safe
>> >> >> >> >> >> side it'd be better to convert the data to average
>> >> >> >> >> >> reference.
>> >> >> >> >> >> In
>> >> >> >> >> >> your
>> >> >> >> >> >> case of a 64 channel system you'd need something like:
>> >> >> >> >> >>
>> >> >> >> >> >> tra = eye(64) - ones(64)/64;
>> >> >> >> >> >>
>> >> >> >> >> >> for the EEG channels (or if you have 65, the same with 65).
>> >> >> >> >> >>
>> >> >> >> >> >> Best,
>> >> >> >> >> >>
>> >> >> >> >> >> Vladimir
>> >> >> >> >> >>
>> >> >> >> >> >> On Tue, Jun 16, 2009 at 12:37 PM, Diane
>> >> >> >> >> >> Whitmer<[log in to unmask]>
>> >> >> >> >> >> wrote:
>> >> >> >> >> >> > Dear SPMers,
>> >> >> >> >> >> >
>> >> >> >> >> >> > I am using SPM8 with EEG data. When I try to compute the
>> >> >> >> >> >> > Inverse
>> >> >> >> >> >> > solution, I
>> >> >> >> >> >> > get the following error message:
>> >> >> >> >> >> >
>> >> >> >> >> >> > Warning: Matrix is singular, close to singular or badly
>> >> >> >> >> >> > scaled.
>> >> >> >> >> >> > Results may be inaccurate. RCOND = NaN.
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> > Does anyone have suggestions for how to debug this?
>> >> >> >> >> >> >
>> >> >> >> >> >> > A subset of these data previously worked for computing an
>> >> >> >> >> >> > Inverse
>> >> >> >> >> >> > Solution.
>> >> >> >> >> >> > One difference with my current dataset is that I have
>> >> >> >> >> >> > re-referenced
>> >> >> >> >> >> > to
>> >> >> >> >> >> > one
>> >> >> >> >> >> > of the EEG channels (because it's not clear that SPM
>> >> >> >> >> >> > selects
>> >> >> >> >> >> > a
>> >> >> >> >> >> > reference
>> >> >> >> >> >> > channel when importing from Biosemi). This may or may not
>> >> >> >> >> >> > be
>> >> >> >> >> >> > related
>> >> >> >> >> >> > to
>> >> >> >> >> >> > the
>> >> >> >> >> >> > problem I'm having.
>> >> >> >> >> >> >
>> >> >> >> >> >> >
>> >> >> >> >> >> > Thank you,
>> >> >> >> >> >> > --
>> >> >> >> >> >> > Diane Whitmer, Ph.D.
>> >> >> >> >> >> > Researcher in Applied Neuroscience
>> >> >> >> >> >> >
>> >> >> >> >> >> > C. de l' Observatori Fabra s/n
>> >> >> >> >> >> > 08035 - Barcelona - Spain
>> >> >> >> >> >> > tel. +34 93 254 03 68
>> >> >> >> >> >> > fax. +34 93 212 64 45
>> >> >> >> >> >> > skype. dwhitmer
>> >> >> >> >> >> > email. [log in to unmask]
>> >> >> >> >> >> > ______________________________________
>> >> >> >> >> >> > STARLAB, Living Science http://www.starlab.es
>> >> >> >> >> >> >
>> >> >> >> >> >> > This e-mail and the attached files contain confidential
>> >> >> >> >> >> > information
>> >> >> >> >> >> > and
>> >> >> >> >> >> > are
>> >> >> >> >> >> > of exclusive use for the addressee. The disclosure, copy
>> >> >> >> >> >> > and
>> >> >> >> >> >> > distribution of
>> >> >> >> >> >> > the present message and its attachments are prohibited.
>> >> >> >> >> >> > If
>> >> >> >> >> >> > you
>> >> >> >> >> >> > are
>> >> >> >> >> >> > not
>> >> >> >> >> >> > the
>> >> >> >> >> >> > intended recipient and you receive this communication, we
>> >> >> >> >> >> > inform
>> >> >> >> >> >> > you
>> >> >> >> >> >> > that it
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>> >> >> >> >> >> > notify
>> >> >> >> >> >> > us
>> >> >> >> >> >> > at
>> >> >> >> >> >> > [log in to unmask] and proceed immediately to delete it.
>> >> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> >
>> >> >> >> >> > --
>> >> >> >> >> > Diane Whitmer, Ph.D.
>> >> >> >> >> > Researcher in Applied Neuroscience
>> >> >> >> >> >
>> >> >> >> >> > C. de l' Observatori Fabra s/n
>> >> >> >> >> > 08035 - Barcelona - Spain
>> >> >> >> >> > tel. +34 93 254 03 68
>> >> >> >> >> > fax. +34 93 212 64 45
>> >> >> >> >> > skype. dwhitmer
>> >> >> >> >> > email. [log in to unmask]
>> >> >> >> >> > ______________________________________
>> >> >> >> >> > STARLAB, Living Science http://www.starlab.es
>> >> >> >> >> >
>> >> >> >> >> > This e-mail and the attached files contain confidential
>> >> >> >> >> > information
>> >> >> >> >> > and
>> >> >> >> >> > are
>> >> >> >> >> > of exclusive use for the addressee. The disclosure, copy and
>> >> >> >> >> > distribution of
>> >> >> >> >> > the present message and its attachments are prohibited. If
>> >> >> >> >> > you
>> >> >> >> >> > are
>> >> >> >> >> > not
>> >> >> >> >> > the
>> >> >> >> >> > intended recipient and you receive this communication, we
>> >> >> >> >> > inform
>> >> >> >> >> > you
>> >> >> >> >> > that it
>> >> >> >> >> > is forbidden by law to read, copy or use it. Please notify
>> >> >> >> >> > us
>> >> >> >> >> > at
>> >> >> >> >> > [log in to unmask] and proceed immediately to delete it.
>> >> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > --
>> >> >> >> > Diane Whitmer, Ph.D.
>> >> >> >> > Researcher in Applied Neuroscience
>> >> >> >> >
>> >> >> >> > C. de l' Observatori Fabra s/n
>> >> >> >> > 08035 - Barcelona - Spain
>> >> >> >> > tel. +34 93 254 03 68
>> >> >> >> > fax. +34 93 212 64 45
>> >> >> >> > skype. dwhitmer
>> >> >> >> > email. [log in to unmask]
>> >> >> >> > ______________________________________
>> >> >> >> > STARLAB, Living Science http://www.starlab.es
>> >> >> >> >
>> >> >> >> > This e-mail and the attached files contain confidential
>> >> >> >> > information
>> >> >> >> > and
>> >> >> >> > are
>> >> >> >> > of exclusive use for the addressee. The disclosure, copy and
>> >> >> >> > distribution of
>> >> >> >> > the present message and its attachments are prohibited. If you
>> >> >> >> > are
>> >> >> >> > not
>> >> >> >> > the
>> >> >> >> > intended recipient and you receive this communication, we
>> >> >> >> > inform
>> >> >> >> > you
>> >> >> >> > that it
>> >> >> >> > is forbidden by law to read, copy or use it. Please notify us
>> >> >> >> > at
>> >> >> >> > [log in to unmask] and proceed immediately to delete it.
>> >> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > --
>> >> >> > Diane Whitmer, Ph.D.
>> >> >> > Researcher in Applied Neuroscience
>> >> >> >
>> >> >> > C. de l' Observatori Fabra s/n
>> >> >> > 08035 - Barcelona - Spain
>> >> >> > tel. +34 93 254 03 68
>> >> >> > fax. +34 93 212 64 45
>> >> >> > skype. dwhitmer
>> >> >> > email. [log in to unmask]
>> >> >> > ______________________________________
>> >> >> > STARLAB, Living Science http://www.starlab.es
>> >> >> >
>> >> >> > This e-mail and the attached files contain confidential
>> >> >> > information
>> >> >> > and
>> >> >> > are
>> >> >> > of exclusive use for the addressee. The disclosure, copy and
>> >> >> > distribution of
>> >> >> > the present message and its attachments are prohibited. If you are
>> >> >> > not
>> >> >> > the
>> >> >> > intended recipient and you receive this communication, we inform
>> >> >> > you
>> >> >> > that it
>> >> >> > is forbidden by law to read, copy or use it. Please notify us at
>> >> >> > [log in to unmask] and proceed immediately to delete it.
>> >> >> >
>> >> >
>> >> >
>> >> >
>> >> > --
>> >> > Diane Whitmer, Ph.D.
>> >> > Researcher in Applied Neuroscience
>> >> >
>> >> > C. de l' Observatori Fabra s/n
>> >> > 08035 - Barcelona - Spain
>> >> > tel. +34 93 254 03 68
>> >> > fax. +34 93 212 64 45
>> >> > skype. dwhitmer
>> >> > email. [log in to unmask]
>> >> > ______________________________________
>> >> > STARLAB, Living Science http://www.starlab.es
>> >> >
>> >> > This e-mail and the attached files contain confidential information
>> >> > and
>> >> > are
>> >> > of exclusive use for the addressee. The disclosure, copy and
>> >> > distribution of
>> >> > the present message and its attachments are prohibited. If you are
>> >> > not
>> >> > the
>> >> > intended recipient and you receive this communication, we inform you
>> >> > that it
>> >> > is forbidden by law to read, copy or use it. Please notify us at
>> >> > [log in to unmask] and proceed immediately to delete it.
>> >> >
>> >
>> >
>> >
>> > --
>> > Diane Whitmer, Ph.D.
>> > Researcher in Applied Neuroscience
>> >
>> > C. de l' Observatori Fabra s/n
>> > 08035 - Barcelona - Spain
>> > tel. +34 93 254 03 68
>> > fax. +34 93 212 64 45
>> > skype. dwhitmer
>> > email. [log in to unmask]
>> > ______________________________________
>> > STARLAB, Living Science http://www.starlab.es
>> >
>> > This e-mail and the attached files contain confidential information and
>> > are
>> > of exclusive use for the addressee. The disclosure, copy and
>> > distribution of
>> > the present message and its attachments are prohibited. If you are not
>> > the
>> > intended recipient and you receive this communication, we inform you
>> > that it
>> > is forbidden by law to read, copy or use it. Please notify us at
>> > [log in to unmask] and proceed immediately to delete it.
>> >
>
>
>
> --
> Diane Whitmer, Ph.D.
> Researcher in Applied Neuroscience
>
> C. de l' Observatori Fabra s/n
> 08035 - Barcelona - Spain
> tel. +34 93 254 03 68
> fax. +34 93 212 64 45
> skype. dwhitmer
> email. [log in to unmask]
> ______________________________________
> STARLAB, Living Science http://www.starlab.es
>
> This e-mail and the attached files contain confidential information and are
> of exclusive use for the addressee. The disclosure, copy and distribution of
> the present message and its attachments are prohibited. If you are not the
> intended recipient and you receive this communication, we inform you that it
> is forbidden by law to read, copy or use it. Please notify us at
> [log in to unmask] and proceed immediately to delete it.
>