Hi

I’ve decided to do the VBM on FA maps with the following pipeline but still I have some points to decide:

1. Eddy and motion correction. I don’t have fieldmaps to make geometric distortion due to susceptibilities changes. I don’t know a method to correct signal loses…
2. Normalization of native images to a standard space using linear affine 12 parameters. This can be done without nonlinear warping to reflect variability in a common standard space, my goal in this step is to make a diffusion template. The possibilities can be:
1. Native b0 ŕ EPI template
2. Native whole head EPI (obtained using the common sequence to functional BOLD imaging) (previously registered to b0 native)  ŕ EPI template

 “I think option a. quarantines better registration of diffusion data to standard space. However, I propose b. because I’m afraid b0 intensity is too low and maybe this can affect the registration process in someway. Furthermore, although one uses a single shot EPI sequence like functional BOLD imaging (which is the of the same modality of EPI template) to obtain b0 image, some differences can be found between b0 and BOLD-EPI that makes me suspect they are not exactly of the same modality (I think, anyway, this can be circumvented using mutual information).

Finally, I can consider, as the reference image or template, the T2 template if this entails better results

3. I’d like to somehow mask images to remove edge effects that arise when a wrong brain extraction is done. This is very important because hyperintensities appear in the edges of the FA maps due to the very noisy nature of diffusion images in voxels outside the brain. In my opinion this is unacceptable for the construction of a template.
1. I can mask the b0 (again the low intensity problem arises). This time I can use BET-FSL or some masking routine in SPM I don’t know.
2. I’ve tried probability segmentations to define automatically an inside brain region (this leave most of the time a fine line of hyperintensity)
4. Once all natives images are in standard space to obtain mean image. This will used as the reference image to re-normalize the diffusion b0 images. In this step, I don’t know if nonlinear warping should be used.

Is there any other step missing here (e.g. intensity correction)?

Please, I’ll appreciate if a hard criticism if done.

Thank you for your time…

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Pedro Antonio Valdés Hernández

Neurophysics Department,

Cuban Neuroscience Center.

Havana City, Cuba.

Phone Number: (537) 2084460

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