JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for SPM Archives


SPM Archives

SPM Archives


SPM@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

SPM Home

SPM Home

SPM  May 2012

SPM May 2012

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: MEG group comparison neuromag

From:

Vladimir Litvak <[log in to unmask]>

Reply-To:

Vladimir Litvak <[log in to unmask]>

Date:

Tue, 8 May 2012 22:51:43 +0100

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (175 lines) , spm_cond_units.m (175 lines) , spm_eeg_invert.m (175 lines) , spm_eeg_lgainmat.m (175 lines)

Dear Stephan and Erick,

Please try the attached fix for the problems with lead field scaling.
It does seem to improve things on our example. It'll be in the next
SPM8 update.

Vladimir

On Thu, May 3, 2012 at 11:48 AM, Erick Britis Ortiz
<[log in to unmask]> wrote:
> Dear Stephan, Vladimir, Rik,
>
> we have a CTF system, but we had a problem that might be related to
> yours. I am taking the opportunity to inform Vladimir too.
>
> The leadfield calculation changed from r4010 to r4290. When the
> preparation steps (forward model, etc) for the inversion are done with
> one version of SPM, but the leadfield calculation is done with another,
> the leadfields might end up with a different scale than if calculated
> with just one version. The values are the same, just multiplied by 10^-10.
>
> This is only noticeable in the group inversion, due to the svd in the
> leadfield realignment. On r4010, the leadfield values are between 1e-2
> and 1, all fine. On r4290, the values drop to around 1e-12, and the
> calculation bumps into floating point precision, resulting in 0 spatial
> modes.
>
> To reproduce it, (1) do a complete inversion with SPM r4010, (2) rename
> the SPMgainmatrix.mat file, (3) re-start MATLAB with SPM r4290, (4)
> re-calculate the leadfields and compare the two.
>
> A quick solution is to erase any stale SPMgainmatrix.mat files and start
> the source localization from scratch again ("clear" it, in the GUI).
> Probably re-doing just the forward model would be enough, but better
> safe than sorry. If even this does not work, I suggest trying with r4010.
>
> Good luck,
> Erick
>
>
> On 2012-05-03 08:14, [log in to unmask] wrote:
>> Hi Vladimir and Rik,
>>
>> Thanks for your fast reply. I will try to use less subjects and see what happens.
>>
>> Best,
>>
>> Stephan
>>
>> ________________________________________________________
>> Stephan Moratti, PhD
>>
>> see also: http://web.me.com/smoratti/
>>
>> Universidad Complutense de Madrid
>> Facultad de Psicología
>> Departamento de Psicología Básica I
>> Campus de Somosaguas
>> 28223 Pozuelo de Alarcón (Madrid)
>> Spain
>>
>> and
>>
>> Center for Biomedical Technology
>> Laboratory for Cognitive and Computational Neuroscience
>> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
>> Campus Montegancedo
>> 28223 Pozuelo de Alarcón (Madrid)
>> Spain
>>
>>
>> email: [log in to unmask]
>> Tel.:    +34 679219982
>>
>> El 02/05/2012, a las 22:17, Rik Henson escribió:
>>
>>>
>>> I can confirm that I also sometimes get 0 spatial modes left when using group inversion for MSP, whether Mags only, Grads only or both (ie it appears to be the group inversion that is problematic). The same data gives reasonable inversions when I use MSP without group inversion (ie individual MSP), or MNM or COH. So it must be a problem with the realignment of leadfields; not the leadfields themselves (and I get the same problem whether I use single-shell or single-sphere forward models).
>>>
>>> Unfortunately I haven't yet tracked down why this happens, because on other Neuromag datasets in the past, the group inversion worked fine. I have confirmed that the spm_eeg_invert function (in which the leadfield realignment is done) has not changed during that time, so I can only assume that something else "deep down" in the forward modelling (eg FieldTrip) functions has changed since then?
>>>
>>> Note that I don't think it can be anything to do with the way the data is preprocessed (eg via SSS or SSP), because the MEG data are not used when realigning the leadfields. (Though note that, even if group inversion did work, any spatial adjustment done to the data, eg via SSS or SSP, should, in principle, also be applied to the forward modelling. I'm not sure what is done with any SSP vectors when SSS is applied, but assume that any such SSP vectors present are applied when the data are converted (via the FieldTrip-MNE FIF-reading functions) - and would hope they are also therefore stored somewhere so FieldTrip can adjust leadfields accordinly, but I think we would need advice from a FieldTrip expert....?)
>>>
>>> Sorry not to be more help - I am still puzzling!
>>>
>>> BW,R
>>>
>>> -------------------------------------------------------
>>> DR RICHARD HENSON
>>> Assistant Director for Neuroimaging
>>> MRC Cognition & Brain Sciences Unit
>>> 15 Chaucer Road
>>> Cambridge, CB2 7EF
>>> England
>>> EMAIL:  [log in to unmask]
>>> URL:    http://www.mrc-cbu.cam.ac.uk/people/rik.henson/personal
>>> TEL     +44 (0)1223 355 294 x501
>>> FAX     +44 (0)1223 359 062
>>> MOB     +44 (0)794 1377 345
>>> -------------------------------------------------------
>>> From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of [log in to unmask] [[log in to unmask]]
>>> Sent: 02 May 2012 19:49
>>> To: [log in to unmask]
>>> Subject: [SPM] MEG group comparison neuromag
>>>
>>> Dear SPM users,
>>>
>>> I tried to do a group inversion with neuromag MEG data (2 conditions, 18 subjects). When I include MEGPLANAR I get 0 spatial modes and NaNs. For the MEG I get 1 spatial mode (if I invert individually I get 66 modes for MEG and 104 modes for MEGPLANAR). So, if I only use MEG to get a solution, I get for all subjects, conditions the same solutions (and a very unlikely one, beam former, MNE and LORETA get visual cortex activity, GS group inversion gets auditory activity that is equal for all conditions and subjects).
>>>
>>> I saw similar postings in the SPM list in 2010 and it was advised to wait for a newer SPM version. I have used the newest 2012 SPM version. I did tSSS with the MEG data, but I do not know if SPM applies the SSP vectors to the data (it shouldn't when using tSSS). Could this be the problem?
>>>
>>> Best,
>>>
>>> Stephan
>>>
>>> ________________________________________________________
>>> Stephan Moratti, PhD
>>>
>>> see also: http://web.me.com/smoratti/
>>>
>>> Universidad Complutense de Madrid
>>> Facultad de Psicología
>>> Departamento de Psicología Básica I
>>> Campus de Somosaguas
>>> 28223 Pozuelo de Alarcón (Madrid)
>>> Spain
>>>
>>> and
>>>
>>> Center for Biomedical Technology
>>> Laboratory for Cognitive and Computational Neuroscience
>>> Parque Científico y Tecnológico de la Universidad Politecnica de Madrid
>>> Campus Montegancedo
>>> 28223 Pozuelo de Alarcón (Madrid)
>>> Spain
>>>
>>>
>>> email: [log in to unmask]
>>> Tel.:    +34 679219982
>>>
>>> El 02/05/2012, a las 20:03, Liam Mason escribió:
>>>
>>>> Hi Carlos,
>>>>
>>>> Did you get any answer of if it is possible to extract %SC from a group of subjects? I'm afraid the only way I know is to do them iteratively as you say. If marsbar is able to do it from a second-level (group) SPM file, then would be keen to know!
>>>>
>>>>
>>>> Liam
>>>>
>>>> ---
>>>> School of Psychological Sciences
>>>> University of Manchester
>>>> 0161 275 2692
>>>>
>>>> ________________________________________
>>>> From: SPM (Statistical Parametric Mapping) [[log in to unmask]] on behalf of Ming-Tsung Tseng [[log in to unmask]]
>>>> Sent: 24 April 2012 18:14
>>>> To: [log in to unmask]
>>>> Subject: Re: [SPM] Compare 2 methods to extract %signal change in MarsBaR
>>>>
>>>> Hi Matthew,
>>>>
>>>> Excellent to get your clear explanation!!
>>>>
>>>> So I can use Method 2 to extract Beta values in a group of subjects, right??
>>>>
>>>> One more question: Since %SC and Beta value can both represent neural response in an ROI, which one is better?......I mean, if I want to extract %SC, I have to use Method 1 which will be performed subject by subject and time-consuming (or any time-saving way to get %SC within many ROIs in a group of subjects)?
>>>>
>>>> Thanks indeed!
>>>>
>>>> Carlos
>>
>>

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

April 2024
March 2024
February 2024
January 2024
December 2023
November 2023
October 2023
September 2023
August 2023
July 2023
June 2023
May 2023
April 2023
March 2023
February 2023
January 2023
December 2022
November 2022
October 2022
September 2022
August 2022
July 2022
June 2022
May 2022
April 2022
March 2022
February 2022
January 2022
December 2021
November 2021
October 2021
September 2021
August 2021
July 2021
June 2021
May 2021
April 2021
March 2021
February 2021
January 2021
December 2020
November 2020
October 2020
September 2020
August 2020
July 2020
June 2020
May 2020
April 2020
March 2020
February 2020
January 2020
December 2019
November 2019
October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007
2006
2005
2004
2003
2002
2001
2000
1999
1998


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

For help and support help@jisc.ac.uk

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager