-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of SPM automatic digest system
Sent: Tuesday, May 17, 2011 4:00 PM
To: [log in to unmask]
Subject: SPM Digest - 16 May 2011 to 17 May 2011 (#2011-145)
There are 12 messages totaling 1451 lines in this issue.
Topics of the day:
1. Batch problem--3D Source Reconstruction
2. Corregistro PET-T1 with DARTEL
3. SPM 2nd level analysis - reg
4. SPM 2nd level analysis-reg
5. Time frequency question
6. slicetiming difficulty
7. After estimation design matrix loses most regressors. (2)
8. SnPM for VBM analysis
9. Correcting for non-stationary smoothnees in vbm
10. Re-Referencing of EEG Data
11. uj in bilinear state equation
----------------------------------------------------------------------
Date: Tue, 17 May 2011 09:31:28 +0800
From: 飞鸟 <[log in to unmask]>
Subject: Re: Batch problem--3D Source Reconstruction
Dear Vladimir,
Thank you very much! May you a happy day!
Haoran.
在 2011-05-16 19:04:19，"Vladimir Litvak" <[log in to unmask]> 写道：
>Dear Haoran,
>
>
>
>On 16 May 2011, at 10:13, "飞鸟" <[log in to unmask]> wrote:
>
>> Dear Vladimir,
>> Your guess was right. I really couldn't do 3D sources reconstruction of that data by GUI. It reminded me ''checkmeeg: data scale missing, assigning default
>> checkmeeg: no fiducials are defined''. Then I did preprocess steps again, and found that I couldn't obtain the fiducials automatically(when I finished Converting step). I checked the other datasets, luckily, they didn't have this problem. I guess there must be some wrongs of my original dataset (only that one), right ?
>
>right
>
>> As for reconstruction batch problem, with the latest version of spm8(4029) and normal dataset, I can do reconstruction by that saved "renconstruction_batch" successfully. Thus, the problems related to reconstruction batch that I confronted previously may result from the different versions of spm8.
>> By the way, in ''MEEG head model specification> EEG head modle'' module, must I specify the ''EEG head modle'' if I just process MEG dataset?
>
>One peculiarity of batch is that when you build the configuration you
>can't use information from the dataset which only becomes available
>when you run the batch. In particular you can't know if the dataset in
>question is EEG or MEG. So don't worry about the EEG head model. If
>your dataset is MEG it will be ignored.
>
>Best,
>
>Vladimir
>
>
>> Thank you very much for helping me solve these tiny problems!
>>
>> Haoran.
>>
>>
>> At 2011-05-16 06:38:23，"Vladimir Litvak" <[log in to unmask]> wrote:
>>
>> >Dear Haoran,
>> >
>> >The problem seems to be not in the batch but in your MEG data (or was
>> >it EEG?). There are no valid fiducials in that dataset. Could you
>> >perform source reconstruction using the GUI? I'd be surprised if you
>> >could. So we need to focus on how to get fiducials into your dataset
>> >and for that you need to tell me more about where that data comes
>> >from.
>> >
>> >Best,
>> >
>> >Vladimir
>> >
>> >2011/5/15 飞鸟 <[log in to unmask]>:
>> >> Dear Vladimir,
>> >> I tried again with the latest version of spm8(4029), the previous problem(
>> >> template=1) disappeared. But this time, I confronted a new problem. It
>> >> reminded me "No executable modules, but still unresolved dependencies or
>> >> incomplete module inputs." But I don't know where the problems are. Could
>> >> you help me see my reconstruction_batch.mat and give me some advice ? Thanks
>> >> a lot.
>> >>
>> >> Haoran.
>> >>
>> >> These code appears in the matlab command window when I ran the batch:
>> >> SPM8: spm_eeg_inv_mesh_ui (v4027) 11:09:13 - 15/05/2011
>> >> ========================================================================
>> >> template: 0
>> >> sMRI: 'D:\Processed\DP01\sKEYAN-0002-00000-000001-01.img,1'
>> >> def: 'D:\Processed\DP01\y_sKEYAN-0002-00000-000001-01.nii'
>> >> Affine: [4x4 double]
>> >> Msize: 2
>> >> tess_mni: [1x1 struct]
>> >> tess_ctx:
>> >> 'D:\Processed\DP01\sKEYAN-0002-00000-000001-01cortex_8196.surf.gii'
>> >> tess_scalp:
>> >> 'D:\Processed\DP01\sKEYAN-0002-00000-000001-01scalp_2562.surf.gii'
>> >> tess_oskull:
>> >> 'D:\Processed\DP01\sKEYAN-0002-00000-000001-01oskull_2562.surf.gii'
>> >> tess_iskull:
>> >> 'D:\Processed\DP01\sKEYAN-0002-00000-000001-01iskull_2562.surf.gii'
>> >> fid: [1x1 struct]
>> >> Failed 'M/EEG head model specification'
>> >> Reference to non-existent field 'fid'.
>> >> In file "C:\Program Files\MATLAB\spm8new\config\spm_cfg_eeg_inv_headmodel.m"
>> >> (v4118), function "specify_headmodel" at line 209.
>> >> No executable modules, but still unresolved dependencies or incomplete
>> >> module inputs.
>> >> The following modules did not run:
>> >> Failed: M/EEG head model specification
>> >> Skipped: M/EEG source inversion
>> >> Skipped: M/EEG inversion results
>> >>
>> >>
>> >> At 2011-05-13 22:06:06，"Vladimir Litvak" <[log in to unmask]
>> >>> wrote:
>> >>
>> >>>Dear Haoran,
>> >>>
>> >>>I tried and everything works fine for me. Make sure your SPM version
>> >>>is up to date and if you can't make it work, send me your saved batch
>> >>>and I'll take another look.
>> >>>
>> >>>Best,
>> >>>
>> >>>Vladimir
>> >>>
>> >>>2011/5/10 飞鸟 <[log in to unmask]>:
>> >>>> Dear SPM's users,
>> >>>> Have you ever used batch interface to do 3D source reconstruction for
>> >>>> EEG/MEG data? I choosed three separate modules "M/EEG head model
>> >>>> specification" "M/EEG source inversion" and "M/EEG inversion results" so as
>> >>>> to reconstruct the sources. In the "M/EEG head model specification" module,
>> >>>> I specified ''Meshes<Meshes source<individual structual image'' and then
>> >>>> selected a mri file named "sDP74-0003-00000-000001-01.img,1". When all was
>> >>>> ready and then I ran the batch, however, I found that it din't excuted the
>> >>>> specified structual image ( as you can see below 'template=1') and the
>> >>>> matlab command window appeared those:
>> >>>>
>> >>>> SPM8: spm_eeg_inv_mesh_ui (v3731) 21:39:06 - 09/05/2011
>> >>>> ========================================================================
>> >>>> template: 1
>> >>>> Affine: [4x4 double]
>> >>>> sMRI: 'C:\Program
>> >>>> Files\MATLAB\toolbox\spm8\canonical\single_subj_T1.nii'
>> >>>> Msize: 2
>> >>>> tess_mni: [1x1 struct]
>> >>>> tess_ctx: 'C:\Program
>> >>>> Files\MATLAB\toolbox\spm8\canonical\cortex_8196.surf.gii'
>> >>>> tess_scalp: 'C:\Program
>> >>>> Files\MATLAB\toolbox\spm8\canonical\scalp_2562.surf.gii'
>> >>>> tess_oskull: 'C:\Program
>> >>>> Files\MATLAB\toolbox\spm8\canonical\oskull_2562.surf.gii'
>> >>>> tess_iskull: 'C:\Program
>> >>>> Files\MATLAB\toolbox\spm8\canonical\iskull_2562.surf.gii'
>> >>>> fid: [1x1 struct]
>> >>>>
>> >>>> I didn't understand why. Anyone who knows the reason ? Thanks very much
>> >>>> for any help !
>> >>>>
>> >>>> --
>> >>>> Haoran LI (MS)
>> >>>> Brain Imaging Lab,
>> >>>> Research Center for Learning Science,
>> >>>> Southeast University
>> >>>> 2 Si Pai Lou , Nanjing, 210096, P.R.China
>> >>>>
>> >>>>
>> >>
>> >>
>> >>
>> >>
>> >>
>>
>>
--
Haoran LI (MS)
Brain Imaging Lab,
Research Center for Learning Science,
Southeast Un
------------------------------
Date: Tue, 17 May 2011 05:10:34 +0100
From: David Yang <[log in to unmask]>
Subject: Re: Corregistro PET-T1 with DARTEL
Dear John:
Thanks for your kind and useful reply.
I wanted to make sure my interpretation was right:
Step 1: was done by SPM function: Coreg:estimate and the registration information would be stored in the header of source images (no other output would be found)
Step 2 and Step 3:just as routine DARTEL process on T1 images
Step4: as in DARTEL toolbox: normalise to MNI space option and use source images (PET) from Step1.
For receptor/transporter binding potential images, I suspected we should choose Preserve Amount in Step 4 according to previous discussion:
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=SPM;f3f7b65.0901
Furthermore, considering the image features of PET or even SPECT images, it might have to smooth such images with large amount (ex 12 mm compared to default 8 mm in DARTEL). I wonder if such was suitable if we wanted to perform further analysis by BPM that used both VBM and PET/SPECT images concurrently as in this subject:
http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=SPM;dd737de1.1012
Thanks for your help~
Sincerely yours,
David
------------------------------
Date: Tue, 17 May 2011 11:45:40 +0530
From: cognitive dept neuro science <[log in to unmask]>
Subject: SPM 2nd level analysis - reg
Dear All,
We are(our team) processing our datas using SPM8. We are able to process
upto first level. We are able to get the activations at the end of first
level result. But we cant further process our second level analysis. Please
help us to process further.
Thanks in advance.
--
Regards,
Cognitive Neurosciences Centre,
Dept of Clinical Psychology,
NIMHANS-Banglore 560 029.
------------------------------
Date: Tue, 17 May 2011 11:59:50 +0530
From: cognitive dept neuro science <[log in to unmask]>
Subject: SPM 2nd level analysis-reg
Dear All,
We are(our team) processing our datas using SPM8. We are able to process
upto first level. We are able to get the activations at the end of first
level result. But we cant further process our second level analysis. Please
help us to process further.
Thanks in advance.
--
Regards,
Cognitive Neurosciences Centre,
Dept of Clinical Psychology,
NIMHANS-Banglore 560 029.
------------------------------
Date: Tue, 17 May 2011 08:08:58 +0100
From: Vladimir Litvak <[log in to unmask]>
Subject: Re: Time frequency question
http://en.wikipedia.org/wiki/Decibel
On Tue, May 17, 2011 at 4:50 AM, Tommy Ng <[log in to unmask]> wrote:
> HI Sir
> Sorry to bother you again, I have a basic question regarding TF analysis in
> SPM.
> As instructed in SPM manual, I averaged TF from single data series using the
> option LogR. The ensuing source power maps appear reasonable but I do not
> know the units of the Z axis. The manual says Db. What is Db?
> Thank you for your time and help.
> Regards
> Tommy Ng
------------------------------
Date: Tue, 17 May 2011 10:20:02 +0100
From: Andreas Finkelmeyer <[log in to unmask]>
Subject: Re: slicetiming difficulty
Check to see if the number of slices of this subject is identical to the other subjects, and as you expect them to be - most likely there are more slices. The easiest way to do this is to check the last number in 'Dimensions', when you use the 'Display' button to look at the image.
Good luck!
===================================================
Andreas Finkelmeyer, Ph.D.
Institute of Neuroscience, Newcastle University
Academic Psychiatry, Building 15, Newcastle General Hospital
Westgate Road, Newcastle NE4 6BE, UK
Tel.: +44 (0)191 256 3296 Fax: +44 (0)191 256 3324
Web: www.ncl.ac.uk/ion
>-----Original Message-----
>From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]
>On Behalf Of Rebecca Ray
>Sent: 16 May 2011 22:44
>To: [log in to unmask]
>Subject: [SPM] slicetiming difficulty
>
>I have successfully preprocessed all of my data with the exception of this one
>subject. Our TR is 2.6 but it changes it to 2.7 and gives the following error
>message:
>
>SPM8: spm_slice_timing (v3756) 16:27:38 - 16/05/2011
>===========================================================
>=============
>Your TR is 2.7
>Failed 'Slice Timing'
>Improper assignment with rectangular empty matrix.
>In file "/Applications/spm8/spm_slice_timing.m" (v3756), function
>"spm_slice_timing" at line 232.
>In file "/Applications/spm8/config/spm_run_st.m" (v2312), function
>"spm_run_st" at line 25.
>
>I have spoken with our physicist who does not use SPM, and he does not
>think it is a problem with the data.
>
>I can display the data prior to slicetiming but not after. After it appears to
>have spit out files but gives an error when you try to display these images:
>Running 'Display Image'
>Image
>"/Users/rebeccaray/Documents/UW_Projects/Vivek/Data_Processing/Raw_
>Data/022_S2/Functionals/Emotion/scan2/agvscan0329.img" can not be
>resampled
>Image
>"/Users/rebeccaray/Documents/UW_Projects/Vivek/Data_Processing/Raw_
>Data/022_S2/Functionals/Emotion/scan2/agvscan0329.img" can not be
>resampled
>Done 'Display Image'
>Done
>
>Any advice would be awesome!
------------------------------
Date: Tue, 17 May 2011 12:51:23 +0100
From: Thomas Nichols <[log in to unmask]>
Subject: Re: After estimation design matrix loses most regressors.
Dear Mike,
Before estimation, the displayed design matrix is original matrix X (with
the exception that DCT drift basis elements aren't shown). After
estimation, the 'filtered and whitened' design matrix (xX.xKXs.X = K*W*X) is
shown. If certain columns appear to be zeroed out by whitening, that is
because the corresponding scans were found to have super-high variance.
(See my earlier post on errors with PET data).
I can't figure out why this is happening, though, as each session's data is
scaled separately. You can check out the scan-by-scan scale factors used to
bring each session to a Grand Mean of 100 by looking at SPM.xGX.gSF; if
there is crazy variation in this (e.g. super-low values for sessions 1 & 3)
it would explain the effect. Then the question is why are the computed
globals so different over sessions... maybe crazy-large artifactual values
in sessions 2, 4, 5,..,8?
Hope this helps with the detective work!
-Tom
On Wed, May 11, 2011 at 12:57 PM, Michael Thomas Smith <
[log in to unmask]> wrote:
> I'm interested in the correlation between a time series and the voxels in
> the brain. To find out more I made a GLM
> (see http://www.sal.mvm.ed.ac.uk/images/problem1.png ).
>
> Before estimation it looks fine (I think?).
>
> During estimation however, 6 of the 8 columns are set to zero (see inset in
> bottom-left corner of the linked image). Just sessions 1 and 3 output beta
> images. There are no errors or warnings expressed during estimation, and the
> matlab output appears ok.
>
> - I've confirmed the number of images in each session is equal to the
> number of values in the .txt regressor files.
> - I've tried adding conditions to each session (just a single event near
> the start of each session) to see if it's the lack of conditions that's
> upsetting SPM. (this didn't make any difference).
> - I've rebuilt the design matrix from scratch by hand, using the interface,
> but that didn't make any difference.
>
> Looking forward to any suggestions!
>
> Thanks,
>
> Mike Smith
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
--
____________________________________________
Thomas Nichols, PhD
Principal Research Fellow, Head of Neuroimaging Statistics
Department of Statistics & Warwick Manufacturing Group
University of Warwick
Coventry CV4 7AL
United Kingdom
Email: [log in to unmask]
Phone, Stats: +44 24761 51086, WMG: +44 24761 50752
Fax: +44 24 7652 4532
------------------------------
Date: Tue, 17 May 2011 09:27:05 -0400
From: "Rajagopalan, Venkateswaran" <[log in to unmask]>
Subject: SnPM for VBM analysis
Dear All,
I am interested in using SnPM for my VBM analysis. I am in the learning process. I am wondering if somebody could help me with the following
I opened up SnPM GUI and opened the setup option and I choose >2 groups Between groups ANOVA 1 scan/subject option since I have 5 groups including control group in total. After I choose my plug a window pops up to open the files so for instance I chose 4 controls (smwrp1 files), 3 from patient group 1, 5 from from patient group 2. Then when I started to enter subject index A A A A B B B C C... the option to enter subject index doesn't seem to stop at the end of 12th index since I chose only 12 subjects data the option to enter subject index keeps going on for ever what am I doing wrong here.
Thanks.
Venkat
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------------------------------
Date: Tue, 17 May 2011 17:45:15 +0200
From: Joana Braga Pereira <[log in to unmask]>
Subject: Re: Correcting for non-stationary smoothnees in vbm
Dear Christian,
I've replaced the cg_spmT2x.m by the one you sent on your previous email.
However, i still get the following error:
Running 'Threshold and transform spmT-maps'
Use local RPV values to correct for non-stationary of smoothness.
Failed 'Threshold and transform spmT-maps'
Subscript indices must either be real positive integers or logicals.
In file "C:\Program Files\spm8\spm8\toolbox\vbm8\cg_spmT2x.m" (v412),
function "cg_spmT2x" at line 335.
Any ideas why this might be happening?
Many thanks!
Joana
2011/5/3 Christian Gaser <[log in to unmask]>
> Dear Aleksander,
>
> Raphael found the bug. I have attached the corrected version. However, it
> is a little bit odd that this failure will occur, because that means that
> your RPV image (Resels per volume) was not correct.
>
> Regards,
>
> Christian
>
> On Tue, 3 May 2011 17:16:48 +0200, [log in to unmask] <[log in to unmask]> wrote:
>
> >Dear Christian,
> >
> >we tried the newest VBM 8 Version r414. We still get following Error
> >
> >Running 'Threshold and transform spmT-maps'
> >Use local RPV values to correct for non-stationary of smoothness.
> >Failed 'Threshold and transform spmT-maps'
> >Undefined function or variable 'V2R'.
> >In file "C:\Program Files\spm8\toolbox\vbm8\cg_spmT2x.m" (v412), function
> "cg_spmT2x" at line 312.
> >
> >The following modules did not run:
> >Failed: Threshold and transform spmT-maps.
> >
> >We do not know if it is a result of an operation error or an error in the
> tool itself?
> >
> >With kind regards
> >
> >Aleksander
> >
> >
> >
> >
> >
> >Dnia 2 maja 2011 22:37 Christian Gaser <[log in to unmask]>
> napisał(a):
> >
> >> Dear Aleksander,
> >>
> >> as Darren assumed there was some debugging code in the function, which I
> forgot to remove. With the newest update r413 this problem should be now
> solved.
> >>
> >> Regards,
> >>
> >> Christian
> >>
> >>
> ____________________________________________________________________________
> >>
> >> Christian Gaser, Ph.D.
> >> Departments of Psychiatry and Neurology
> >> Friedrich-Schiller-University of Jena
> >> Jahnstrasse 3, D-07743 Jena, Germany
> >> Tel: ++49-3641-934752 Fax: ++49-3641-934755
> >> e-mail: [log in to unmask]
> >> http://dbm.neuro.uni-jena.de
> >>
> >>
> >> On Wed, 27 Apr 2011 11:13:34 +0200, [log in to unmask] <[log in to unmask]> wrote:
> >>
> >> >Hallo,
> >> >
> >> >we are trying to correct for non-stationary of smoothness
> >> >and we get following error report
> >> >
> >> >Use local RPV values to correct for non-stationary of smoothness.
> >> >Failed 'Threshold and transform spmT-maps'
> >> >Undefined function or variable 'K'.
> >> >In file "C:\Program Files\spm8\toolbox\vbm8\cg_spmT2x.m" (v404),
> function
> >> >"cg_spmT2x" at line 321.
> >> >
> >> >The following modules did not run:
> >> >Failed: Threshold and transform spmT-maps
> >> >
> >> >
> >> >We found this :
> >> >"Hi, I have removed the interface to the non-stationarity correction in
> >> >VBM8 because
> >> >of the interferences with the SPM8 GUI. However, there is still a
> hidden
> >> >option if
> >> >you use the conversion tools for transforming and thresholding T-or
> >> >F-maps:
> >> >VBM8|Data presentation|Threshodl and transform T-maps"
> >> >
> >> >And we followed this sequence
> >> >
> >> >The non-stationary cluster correction in VBM8 can be
> >> >implemented
> >> >by the following sequence of menu steps:
> >> >Toolbox > VBM8 > Data presentation > Threshold and transform spmT-maps
> >
> >> >.Cluster
> >> >extent threshold > ..k-value > ...Correct for non-isotropic smoothness
> >> >yes.
> >> >
> >> >but without success.
> >> >
> >> >Do you have some experience with this part of the Vbm8 tool?
> >> >
> >> >We would be thankful for any help.
> >> >
> >> >With kind regards
> >> >
> >> >Aleksander
> >>
>
>
------------------------------
Date: Tue, 17 May 2011 18:16:59 +0100
From: Michael Thomas Smith <[log in to unmask]>
Subject: Re: After estimation design matrix loses most regressors.
Thanks for the reply.
It seems likely it's something to do with my install of SPM, as Thomas
was able to run exactly the same job on his computer and get the
correct result. I'll reinstall SPM and try again. (by the way: I found
adding extra regressors caused the left-out columns to change...all
very weird).
Thanks again for the suggestions and help,
I'll be back with more questions if the reinstall doesn't work!
Mike.
Quoting Thomas Nichols <[log in to unmask]> on Tue, 17 May 2011
12:51:23 +0100:
> Dear Mike,
>
> Before estimation, the displayed design matrix is original matrix X (with
> the exception that DCT drift basis elements aren't shown). After
> estimation, the 'filtered and whitened' design matrix (xX.xKXs.X = K*W*X) is
> shown. If certain columns appear to be zeroed out by whitening, that is
> because the corresponding scans were found to have super-high variance.
> (See my earlier post on errors with PET data).
>
> I can't figure out why this is happening, though, as each session's data is
> scaled separately. You can check out the scan-by-scan scale factors used to
> bring each session to a Grand Mean of 100 by looking at SPM.xGX.gSF; if
> there is crazy variation in this (e.g. super-low values for sessions 1 & 3)
> it would explain the effect. Then the question is why are the computed
> globals so different over sessions... maybe crazy-large artifactual values
> in sessions 2, 4, 5,..,8?
>
> Hope this helps with the detective work!
>
> -Tom
>
>
> On Wed, May 11, 2011 at 12:57 PM, Michael Thomas Smith <
> [log in to unmask]> wrote:
>
>> I'm interested in the correlation between a time series and the voxels in
>> the brain. To find out more I made a GLM
>> (see http://www.sal.mvm.ed.ac.uk/images/problem1.png ).
>>
>> Before estimation it looks fine (I think?).
>>
>> During estimation however, 6 of the 8 columns are set to zero (see inset in
>> bottom-left corner of the linked image). Just sessions 1 and 3 output beta
>> images. There are no errors or warnings expressed during estimation, and the
>> matlab output appears ok.
>>
>> - I've confirmed the number of images in each session is equal to the
>> number of values in the .txt regressor files.
>> - I've tried adding conditions to each session (just a single event near
>> the start of each session) to see if it's the lack of conditions that's
>> upsetting SPM. (this didn't make any difference).
>> - I've rebuilt the design matrix from scratch by hand, using the interface,
>> but that didn't make any difference.
>>
>> Looking forward to any suggestions!
>>
>> Thanks,
>>
>> Mike Smith
>>
>> --
>> The University of Edinburgh is a charitable body, registered in
>> Scotland, with registration number SC005336.
>>
>
>
>
> --
> ____________________________________________
> Thomas Nichols, PhD
> Principal Research Fellow, Head of Neuroimaging Statistics
> Department of Statistics & Warwick Manufacturing Group
> University of Warwick
> Coventry CV4 7AL
> United Kingdom
>
> Email: [log in to unmask]
> Phone, Stats: +44 24761 51086, WMG: +44 24761 50752
> Fax: +44 24 7652 4532
>
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
------------------------------
Date: Tue, 17 May 2011 21:53:26 +0100
From: Vladimir Litvak <[log in to unmask]>
Subject: Re: Re-Referencing of EEG Data
Dear Urs,
On Tue, May 17, 2011 at 10:50 AM, Urs Bachofner <[log in to unmask]> wrote:
> I have a question regarding the concept of EEG data Re-referencing in Spm8.
> The way I see it, re-referencing is a very important step prior to Source
> Analysis. To get useful data, the Signals should be re-referenced to
> average.
> According to the SPM8 Manual P. 110 we can use spm_eeg_montage to do this.
>
> The data I'd like to process is recorded with a 128-channel EEG-net with the
> reference electrode at CZ.
> According to the SPM8 Manual, for average reference the matrix should have
> (N-1)/N at the diagonal and -1/N elsewhere.
> In my case this results in 0.9921875 at the diagonal and -0.0078125
> elsewhere.
>
> Two questions:
> 1. These numbers are so close to the original matrix (1 at diagonal and 0
> elsewhere) which is said to not change anything. Is this matrix correct?
>
Yes, it's all OK. The more electrodes you have the closer the average
will be to zero but remember that the actual values also depend on the
data, not only on the weights so you should still re-reference.
> 2. Since electrodes that are closer to the reference (in this case CZ) have
> a higher amplitude recorded, shouldn't such electrodes be weighted
> differently than electrodes that are more distant to CZ? Am I missing the
> point here?
>
>
No, the average reference is just what it is, every channel minus the
average of all channels. It does not depend on where the original
reference is.
> And finally, besides Filtering, epoching, Artefact Detection (removing bad
> channels and bad trials), Re-referencing, and baseline correction are there
> other preprocessing steps that are necessary to get good data from my evoked
> potentials?
No, these are the basic steps. You might try using the robust
averaging option. Also there is an option in MEEGTools for correcting
eye blinks. You might or might not need it depending on your data.
> And is there a certain order in which these steps should be
> executed?
>
I've just presented a slide about that at the SPM course last week.
Basically it says the following:
----
Considerations for order of processing steps:
It’s better to filter before epoching unless only small part of the
data is relevant. As an alternative one could pad the epochs of
interest with extra data and discard it later.
Downsampling speeds up the other steps and reduces disk space usage,
but it involves low-pass filtering and...
Low-pass or band-pass filtering before high-pass can generate ringing
at the edges, which is especially problematic for epoched data. So
high-pass should come first, but...
Only some channel types (EEG, MEG, LFP etc.) are filtered. So channel
types should be set correctly first (Prepare, Montage).
---
Best,
Vladimir
> Thank you very much for you help.
>
>
>
>
------------------------------
Date: Tue, 17 May 2011 16:47:10 -0400
From: Mobin Anandwala <[log in to unmask]>
Subject: uj in bilinear state equation
Good Afternoon
This is Mobin Anandwala and I have a question regarding the variable uj in
the bilinear state equation. The equation as stated is z' = (A +
sigma(uj*Bj))*z + Cu. As I understand the u vector times the C matrix is a
vector consisting of input functions. My question is that since the u
vector consists of input functions is the uj variable a scalar that is the
maximum of the input function or is it a vector? When I tried to use uj as
a vector I obtained a matrix multiplication error in Matlab with Bj as the
dimensions did not match (u being an n x 1 vector and Bj being 4 x 4). I am
currently using uj as a scalar constant with it being the maximum of input
function (current data that I have has u2(t) in the u vector and the uj
being its maximum).
Thank you
Mobin Anandwala
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End of SPM Digest - 16 May 2011 to 17 May 2011 (#2011-145)
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