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  April 2008

SPM April 2008

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: DARTEL: Longitudinal data analysis

From:

Simone Reinders <[log in to unmask]>

Reply-To:

Simone Reinders <[log in to unmask]>

Date:

Mon, 14 Apr 2008 12:57:45 +0100

Content-Type:

multipart/mixed

Parts/Attachments:

Parts/Attachments

text/plain (154 lines) , batch_dartel_phase1.m (1 lines)

Dear all,

To make DARTEL-life even easier I have attached a batch script for
phase 1 of the longitudinal data processing.

Kind regards,

Simone Reinders, PhD
King's College London
Institute of Psychiatry (IoP)


On Wed, Apr 2, 2008 at 7:32 PM, John Ashburner <[log in to unmask]> wrote:
> I would suggest some slight changes to make life easier:
>  1) Within the DARTEL code, there is some spatial smoothing of the iteratively
>  generated template.  I would suggest reducing the amount of smoothing, as it
>  is generally easier to obtain a better overlap of serial scans than for
>  cross-sectional data.  You may even wish to set the "Smoothing Parameter" to
>  "None".
>  2) Specify a subject-specific template name when you run DARTEL within
>  subject.
>  3) Generate modulated warped GM using the within subject flow fields.  These
>  should be in alignment with the subject-specific template (mwc1BL and
>  mwc1FU).  This template will be half-way between the BL and FU scans, so
>  there should be less bias in terms of whether BL is warped to FU, or vica
>  verca.
>
>  I haven't tested this, but I think it should then be possible to use the
>  Template data for each subject to register all the within subject data
>  together.  Note that the template data has multiple volumes in the same file,
>  so you'll need to change the volume selector (usually set to 1) so that the
>  second volume could be selected.  If this does not work, then you may need to
>  seperate the templates into their individual volumes (ie make two 3D files
>  from a 4D file). Once you have the inter-subject flow fields, then you can
>  use then to generate mwmwc1BL and mwmwc1FU files.  These can then be
>  smoothed, prior to doing some form of paired t-test analysis.
>
>  I hope the above makes sense, and works.  It is a bit messy, and I will try to
>  get around to making it easier to work with serial scans.
>
>  Best regards,
>  -John
>
>
>
>
>  On Tuesday 01 April 2008 16:11, Simone Reinders wrote:
>  > Dear John / DARTEL users,
>  >
>  > To analyze a longitudinal dataset (baseline = BL and Followup = FU) I
>  > would like to use DARTEL. I am trying to follow the steps as offered
>  > in the paper by Kipps et al. 2005 (JNNP) and to interpret them in a
>  > DARTEL manner.
>  >
>  > I have included my steps in detail below.
>  >
>  > I would like to obtain the Jacobian determinant (step 3)) of the flow
>  > field that maps BL into FU, but the output of step 2) gives me only a
>  > deformation field while the input to obtain a Jacobian determinant is
>  > a flow field.
>  >
>  > Is there a way to create a flow field (instead of a deformation field)
>  > that that maps BL into FU which can be used as input to the Jacobian
>  > step?
>  >
>  > Or am I completely on the wrong track?
>  >
>  > Thank you,
>  >   Simone.
>  >
>  > Simone Reinders, PhD
>  > King's College London
>  > Institute of Psychiatry (IoP)
>  >
>  >
>  >
>  >
>  > Page 652 of Kipps paper interpreted in DARTEL:
>  >
>  > 1) Both BL and FU images are manually reoriented. The BL is
>  > coregistered to the FU, with FU being the reference image and no
>  > reslicing.
>  >
>  > *) Initial DARTEL steps:
>  > a) Create scan specific *_seg_sn.mat files for both FU and BL as
>  > desribed in section 1.1 of the DARTEL manual
>  > b) Perform the 'Initial Import' step for both BL and FU both grey and
>  > white matter, creating rc1*.nii and the rc2*.nii files.
>  >
>  > 2) Find subject specific warping/flow fields that warp BL to match FU
>  > within subject.
>  > a) Run DARTEL (create Template) with the subject specific imported
>  > data of the FU and the BL scan (section 1.4 of the DARTEL manual).
>  > * Run DARTEL (create Template)
>  >  - Images
>  >    * Images: Select all the rc1*.nii files 1 for FU and 1 for BL (from
>  > step *)b)), for e.g subject pp1.
>  >    * Images: Select all the rc2*.nii files 1 for FU and 1 for BL for pp1.
>  > This will create two flow fields u_rc1_pp1FU*.nii and u_rc1_pp1BL*.nii.
>  > The name of the flow field is 'u_rc1*' but it is the flow field for
>  > both the rc1 and rc2 images.
>  > b)  Compose the resulting deformations:
>  > TASKS -> utils -> Deformations
>  > * Deformations
>  >   - Composition
>  >     * DARTEL flow
>  >       - Flow field: Specify the u_rc1_pp1BL*.nii flow field.
>  >       - Forward/Backwards: Backward.
>  >       - Time Steps: Usually 64.
>  >     * DARTEL flow
>  >       - Flow field: Specify the u_rc1_pp1FU*.nii flow field.
>  >       - Forward/Backwards: Forward.
>  >       - Time Steps: Usually 64.
>  >     * Identity
>  >       - Image to base Id on: Specify the imported data of FU.nii
>  > (i.e.the rc1_FU and rc2_FU)
>  >   - Save composed deformations as a file 'y_BLtoFUpp1'
>  >     Note: y is a deformation field not a flow field.
>  >
>  > 3) Obtain Jacobian determinant from the deformation/flow field
>  > generated in 2) via DARTEL
>  > Task -> Tools -> DARTEL tools-> Jacobian determinants
>  > This is where I would like to use the flow field for 'y', creating
>  > jac_y*.nii files.
>  >
>  > ... if I have the Jacobian determinants I would like to proceed with:
>  >
>  > 4) These are the FU files from the "Initial Import" stage (from *)b), i.e.
>  > the rc1*.nii and the rc2*.nii files.
>  >
>  > 5) Create customised template on the basis of all FU scans only
>  > * Run DARTEL (create Template)
>  >  - Images
>  >    * Images: Select all the rc1*.nii files for FU.
>  >    * Images: Select all the rc2*.nii files for FU.
>  > This will create FU flow fields u_rc1_*FU*.nii and a customized
>  > template on the basis of FU scans only.
>  >
>  > 6) Create warped images (DARTEL instructions: page 4) by applying the flow
>  > field from step 5) onto the FU images from 4) and on the Jacobian
>  > jac_y*.nii file from step 3) this creates wrc*.nii and wjac_y*.nii images
>  > (all subject specific)
>  >
>  > 7) multiply the wrc1*.nii and the wrc2*.nii with the wjac_y*.nii images
>  > (subject specific) => this gives a measure of tissue specific volume change
>  > from BL to FU, i.e. over time.
>  >
>  > 8) This step from the Kipps 2005 paper is superfluous when using
>  > DARTEL but I might want to transform the results from 7) into MNI
>  > space.
>
>

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

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