Thanks Laurrence for a wonder tutorial, and thanks Vladimir for pointing to
it. It works great for the most part. I say that because I am running into
two problems:
1. I have version 4010 of spm8 but I don't have "view_spatial_confounds.m".
Is there a more recent upgrade that should have this script?
2. For some of the subject data, the
'remove_eyeblink_topography_walkthrough.m' script gives me the following
error:
=======================================================================
??? Index exceeds matrix dimensions.
Error in ==> spm_eeg_spatial_confounds at 166
sconf.coeff(sel1, :) = U(sel2, 1:S.ncomp);
Error in ==> remove_eyeblink_topography_walkthrough at 87
D = spm_eeg_spatial_confounds(S);
but for others it doesn't. How could this be? Both subjects data are similar
in the way they are acquired.
Any help would be much appreciated.
Thanks
- Muhammad
On Wed, Dec 1, 2010 at 9:29 AM, Vladimir Litvak
<[log in to unmask]>wrote:
> Dear Muhammad and other users interested in the topography-based
> artefact correction,
>
> Laurence Hunt prepared a tutorial for artefact detection and rejection
> in SPM and has kindly made it available on
> http://www.fmrib.ox.ac.uk/~woolrich/artifact_session.zip . The file
> contains example data, code and a tutorial for using them. Enjoy and
> thanks again to Laurence.
>
> Best,
>
> Vladimir
>
>
>
> On Wed, Dec 1, 2010 at 10:42 AM, Vladimir Litvak
> <[log in to unmask]> wrote:
> > Dear Muhammad,
> >
> > You can put it before this part. Just note that usually the file you
> > would use to define spatial confounds is not the same file that you
> > correct. The former would be an averaged eyeblink file and the latter
> > your actual dataset of interest. The head model should be in this
> > second dataset.
> >
> > Best,
> >
> > Vladimir
> >
> > On Wed, Dec 1, 2010 at 4:21 AM, MP <[log in to unmask]> wrote:
> >> Hi Vladimir,
> >> Thanks so much for your detailed response. I am now able to generate the
> >> script for the 3D head model. My follow up question to you is, where
> exactly
> >> should I insert it in the eye blink correction routine?
> >> Currently the eye blink removal section of the script looks like the
> >> following:
> >> % Eye Blink Correction
> >> S = [];
> >> S.D = fullname6;
> >> S.method = 'SVD';
> >> S.timewin = [-0.498
> >> 2];
> >> S.ncomp = 2;
> >> D = spm_eeg_spatial_confounds(S);
> >> save(D);
> >> S = [];
> >> S.D = fullname6;
> >> S.correction = 'Berg';
> >> D = spm_eeg_correct_sensor_data(S);
> >> save (D);
> >>
> >> Where should I insert the 3D Head modelling script?
> >> Thanks
> >> - Muhammad
> >>
> >>
> >> On Tue, Nov 30, 2010 at 5:54 AM, Vladimir Litvak <
> [log in to unmask]>
> >> wrote:
> >>>
> >>> Dear Muhammad,
> >>>
> >>> Press the 'Batch' button, go to SPM->M/EEG->M/EEG Source
> >>> reconstruction->M/EEG head model specification
> >>>
> >>> Then you need to specify the configuration. The parameters are the
> >>> same as in 3D source reconstruction window. Once you specify a
> >>> complete configuration that can run (the triangle at the top turns
> >>> grin) you can go to File->Save batch as script and save your
> >>> configuration as an .m file. You can then modify the code if necessary
> >>> and add it to your script.
> >>>
> >>> Best,
> >>>
> >>> Vladimir
> >>>
> >>>
> >>> On Mon, Nov 29, 2010 at 6:47 PM, MP <[log in to unmask]> wrote:
> >>> > Hi Vladimir,
> >>> > Many thanks for your help. Could you please guide how can I
> pre-compute
> >>> > the
> >>> > head model for my dataset using SPM batch tool? I want to do this so
> >>> > that I
> >>> > can include the eye-blink correction using Berg algorithm in a
> script.
> >>> > Thanks,
> >>> > - Muhammad
> >>> >
> >>> > On Sat, Nov 13, 2010 at 7:48 AM, Vladimir Litvak
> >>> > <[log in to unmask]>
> >>> > wrote:
> >>> >>
> >>> >> Dear Muhammad,
> >>> >>
> >>> >> On Sat, Nov 13, 2010 at 3:46 AM, MP <[log in to unmask]> wrote:
> >>> >> > Hello all,
> >>> >> > I am doing eye-blink correction through Berg algorithm. I have a
> >>> >> > couple
> >>> >> > of
> >>> >> > questions in this regard:
> >>> >> > 1. Once the data has been run through the Berg algorithm, is the
> >>> >> > output
> >>> >> > data
> >>> >> > corrected for the eye-blinks, or is there anything that needs to
> be
> >>> >> > done?
> >>> >>
> >>> >> If you've done everything correctly the data is corrected. If it's
> >>> >> continuous data you could average it around eyeblinks again to make
> >>> >> sure they are gone.
> >>> >>
> >>> >> > 2. While running the Berg algorithm, a prompt comes up asking
> "Which
> >>> >> > Head
> >>> >> > Model?" for the MEEG/MRI coregistration. Which script is this
> prompt
> >>> >> > coming
> >>> >> > from?
> >>> >>
> >>> >> Head model is necessary for the 'Berg' option (but not for SSP)
> >>> >> because Berg algorithm uses lead fields of cortical sources. If you
> >>> >> want to batch it you can pre-compute the head model for your dataset
> >>> >> using the batch tool before correcting it.
> >>> >>
> >>> >> > 3. How does the Berg algorithm affect the spectral information in
> the
> >>> >> > data?
> >>> >> > Is it OK to do TF-decomposition and then stat analysis on this
> data?
> >>> >>
> >>> >> In principle it is OK, but it depends on the question and the data
> so
> >>> >> you should still be careful. The principles of this correction are
> >>> >> very similar to those of ICA and ICA is very frequently used for
> >>> >> removing eye blinks prior to all kinds of analyses so you can use
> the
> >>> >> ICA literature as a precedent. In any case perhaps you should repeat
> >>> >> your analysis with and without eye blink correction and convince
> >>> >> yourself that the differences you see can be attributed to eye blink
> >>> >> removal.
> >>> >>
> >>> >> Best,
> >>> >>
> >>> >> Vladimir
> >>> >>
> >>> >>
> >>> >> > Thanks
> >>> >> > - Muhammad
> >>> >> >
> >>> >> >
> >>> >> > On Fri, Nov 12, 2010 at 12:08 PM, Vladimir Litvak
> >>> >> > <[log in to unmask]> wrote:
> >>> >> >>
> >>> >> >> No, this function is used for detecting eyeblinks in continuous
> data
> >>> >> >> as part of eyeblink correction procedure. See
> >>> >> >>
> >>> >> >> https://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=SPM;adf47ab2.1007
> >>> >> >>
> >>> >> >> Vladimir
> >>> >> >>
> >>> >> >> On Fri, Nov 12, 2010 at 5:02 PM, MP <[log in to unmask]> wrote:
> >>> >> >> > Hi all,
> >>> >> >> > It may be a very naive question, but does
> >>> >> >> > 'spm_eeg_detect_eyeblinks' remove
> >>> >> >> > the eye-blinks after detecting them?
> >>> >> >> > Thanks
> >>> >> >> > - Muhammad
> >>> >> >
> >>> >> >
> >>> >
> >>> >
> >>
> >>
> >
>
