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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