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SPM  April 2008

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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:

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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.
>
>

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