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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.