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Subject:

apply deformations VBM8/deformation utility

From:

Michel Grothe <[log in to unmask]>

Reply-To:

Michel Grothe <[log in to unmask]>

Date:

Fri, 6 May 2011 14:16:19 +0100

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text/plain

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Parts/Attachments

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Dear SPM-Experts (especially John and Christian :-)),

I´m using DARTEL for intra- and subsequent inter-subject alignment of VBM8-segments in a longitudinal study design. Segments (Intra-subject bias-corrected) are written out as native (p1, p2, p3) and DARTEL-imported/rigidly aligned (rp1, rp2) images. Latter are used for DARTEL intra-subject alignment in SPM8 (create Template, rp1 and rp2 of BL and FU image; smoothing set to zero) and the resulting intra-subject (half-way) DARTEL_6-templates of all subjects are used for inter-subject alignment.

To reduce interpolation artifacts I aim to combine the individual intra-subject flow-fields (that map to the subject-specific DARTEL template) with the inter-subject flow-fields (subject-specific DARTEL_6 to group DARTEL-template) and apply just one warp. When specifying the flow-field combination in the Deformation Utility as outlined in the DARTEL-manual (i.e. first (top) the intra-subject and second (bottom) the inter-subject flow, both backwards) I get a y-field that accomplishes the desired warp from native VBM8-segment to the group DARTEL template (here I specify the p*-segments; the information about the rigid-transform of the rp*-images seems to get lost by combining the flow-fields, resulting in shifted/rotated wrp*-images compared to wp*-images and the group DARTEL-template respectively).

So far so good, but now I want to have the images modulated (i.e. mwp*), which seems not to be possible with the Deformations Utility and brings me back to the VBM8-toolbox 'apply deformations'-tool. The unmodulated warp of this tool seems to be identical to the unmodulated warp of the Deformation Utility, BUT voxel-values of the modulated warped segment are all negative (and 0 outside). Given that I´ve succesfully used the VBM8 'apply deformations'-tool with modulation in previous studies it might be a bug that came with the last update. So I repeated the warp with an earlier version of the VBM8-toolbox (which I had stored for reproducibility of previous studies), resulting in the following error:

Running 'Apply Deformations'
Failed  'Apply Deformations'
Undefined function or method 'spm_def2det' for input arguments of type 'single'.
In file "D:\spm8\toolbox\vbm8\cg_vbm8_defs.m" (v266), function "apply_def" at line 52.
In file "D:\spm8\toolbox\vbm8\cg_vbm8_defs.m" (v266), function "cg_vbm8_defs" at line 13.

The following modules did not run:
Failed: Apply Deformations

Any idea what might have gone wrong here? Is there a fix for this or will I have to stick to the old approach of 'double-warping' and live with interpolation effects?

Any help will be highly appreciated.
Best regards,
Michel    

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