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:

Monospaced Font

LISTSERV Archives

LISTSERV Archives

SPM Home

SPM Home

SPM  May 2010

SPM May 2010

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: Beta Version of VBM8 Toolbox

From:

Christian Gaser <[log in to unmask]>

Reply-To:

Christian Gaser <[log in to unmask]>

Date:

Mon, 17 May 2010 16:49:18 +0100

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (154 lines)

On Mon, 17 May 2010 17:20:01 +0200, michel grothe <[log in to unmask]> wrote:

Dear Michel,

>
>Dear Mr. Gaser,
>
>thank you very much for your fast reply. However, I guess that I have to
> reformulate my second question:
>
>
>
>How are the jacobian maps computed? As far as I understand the
>registration in VBM8 it involves an initial affine registration to MNI
>space and subsequent Dartel warping of the GM+WM segments (in MNI space)
> to the IXI-DARTEL-Templates (in MNI space). This would mean that the
>Dartel-flow-fields just model remaining non-linear effects. Are the
>Jacobians derived from these Dartel-flow-fields (which would mean that
>global head size is already accounted for in the Jacobian maps, much
>like the m0-modulation) or are they derived from a composition of the
>initial affine registration and the Dartel-warps? In the latter case the
> jacobians would represent volumetric changes from native space to the
>IXI-Dartel-template in MNI space, similar to modulated
>(affine+non-linear) tissue segments. Given that the VBM8-GUI just gives
>the options "none" and "modulated" for Jacobian maps I�m a bit confused
>about the "modulation" of the Jacobians.
>
The jacobians are estimated using only the non-linear terms of the spatial normalization. No additional composition with the affine term is applied. The composition with the affine term is only considered if you save modulated image and the option "affine + non-linear" is selected. This is different from John's approach, but as you already assumed it accounts for different brain/head sizes and simplifies the statistical analysis. It is equivalent to a proportional scaling with the (inverse) scaling factor of the affine transformation in the statistical analysis.

Regards,

Christian
____________________________________________________________________________

Christian Gaser, Ph.D.
Assistant Professor of Computational Neuroscience
Department of Psychiatry
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
>
>
>
>Best regards,
>
>Michel
>
>> Date: Mon, 17 May 2010 06:56:14 +0100
>> From: [log in to unmask]
>> Subject: Re: Beta Version of VBM8 Toolbox
>> To: [log in to unmask]; [log in to unmask]
>> CC: [log in to unmask]
>>
>> On Mon, 17 May 2010 00:39:28 +0200, michel grothe <[log in to unmask]> wrote:
>>
>> >
>> >Dear Mr. Gaser,
>> >
>> >I have some additional questions on the new VBM8 Toolbox.
>> >
>> >1. Which tissue-types are used for the Dartel-normalisation?
>> GM + WM, same as standard Dartel approach
>>
>> >
>> >2. How are the Jacobians modulated? Am I right in assuming that the
>> >initial affine transformation to MNI space is used for that
>> >normalisation and hence does not involve non-linear components? If so,
>> >is there a possibility to get unmodulated jacobians in MNI space, so
>> >that global head size is already accounted for?
>> Check my website for more information:
>> http://dbm.neuro.uni-jena.de/vbm/segmentation/modulation/
>>
>> If you want modulated images, where global head size is corrected for you can use the modulation for non-linear effects only (which is the default). This will be indicated by a prepending "m0" instead of "m". The advantage of VBM8 Dartel integration is that no additional steps for MNI normalization and corrections are necessary.
>>
>> Regards,
>>
>> Christian
>>
>> ____________________________________________________________________________
>>
>> Christian Gaser, Ph.D.
>> Assistant Professor of Computational Neuroscience
>> Department of Psychiatry
>> 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
>>
>>
>> >
>> >
>> >
>> >Thanks for this very helpful toolbox.
>> >
>> >
>> >
>> >Best regards,
>> >
>> >Michel Grothe
>> >
>> >> Date: Sun, 16 May 2010 23:15:18 +0100
>> >> From: [log in to unmask]
>> >> Subject: Re: [SPM] Beta Version of VBM8 Toolbox
>> >> To: [log in to unmask]
>> >>
>> >> Dear Paul,
>> >>
>> >> > Thanks for your toolbox. I have some questions about parameter setting
>> >> >
>> >> > 1. How to change DARTEL export image voxel size, i think the default setting about DARTEL export image is 1.5 cubic
>> >> The voxel size is always set to the voxel size of the tissue probability map (TPM) image. However, if you don't need a customized Dartel template you can use the Dartel approach, which is integrated in VBM8. This Dartel approach will use the Dartel MNI template provided with VBM8 and no additional export or Dartel use is neeeded.
>> >>
>> >> >
>> >> > 2. How to change HMRF weighting ?
>> >> > (In VBM5, we can choose different HMRF weighting in GUI. If i want to use iterative HMRF weighting, how can we choose in this version?)
>> >> In VBM8 two de-noising techniques are used. The first is a non-local means filter as preprocessing step. The filter size is automatically estimated based on the local variance of your image. The second is a MRF, which is integrated in the segmentation process. Again the weighting is now internally estimated based on the noise in your image. However, both approaches can be weighted. The non-local means filter is by default weighted by 0.7, which shows best performance for segmentation. The weighting for the MRF is fixed to 0.15. Both values are optimal for a large variety of data and usually it is not necessary to change the weighting. The weighting can be rather used to deselect the filter by setting the weighting to 0. Anyway, I have now added the option to change both weightings. This will also solve some problems with batch files, where changes of these parameters in cg_vbm8_defaults.m were not considered. Thanks to Jose V. Manjon for pointing to that problem.
>> >> The new version can be downloaded at:
>> >> http://dbm.neuro.uni-jena.de/vbm8/vbm8_r331.zip
>> >>
>> >> Or simply use the update function in VBM8.
>> >>
>> >> Regards,
>> >>
>> >> Christian
>> >>
>> >> ____________________________________________________________________________
>> >>
>> >> Christian Gaser, Ph.D.
>> >> Assistant Professor of Computational Neuroscience
>> >> Department of Psychiatry
>> >> 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
>> >>
>> >> >
>> >> > Best
>> >> >
>> >> > Paul
>> >
>> >_________________________________________________________________
>> >http://redirect.gimas.net/?n=M1004xSkyDrive2
>> >Ihre Daten brauchen Platz? SkyDrive gibt Ihnen 25 GB - gratis!
>>
>>
>
>_________________________________________________________________
>http://redirect.gimas.net/?n=M1004xWin72
>Windows 7 - Alles was Du brauchst und noch viel mehr!

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

May 2024
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