Hi Saad, thanks for the first suggestion, stupid of me not to think about this.
I am not sure I understand the second point, though. What does probtrackx actually do? The probabilities are saved for each voxel in the diffusion space of each individual by bedpost. By normalizing to a template, don't we run the same problem as with the normalization of raw acquisitions, where the bmatrix would have to be adjusted in order to take into account rotation, shear and interpolation effects on the directionality of the vectors?
A related query is the following. All our DTI scans have been corrected for epi distortion with fieldmaps. However, for some we are missing high resolution structurals. What would be the best way to normalize to the MNI template? Use the undistorted b0, the FA image or the magnitude images from the fieldmaps we acquired (they have the same 2 mm isotropic resolution than the DTI scans)? And what template combination would be recommended? For example, do you know whether a T2MNI to b0 registration works better than a T1MNI to FA or field-map magnitude image?
Thanks for your help, Stefano Marenco
From: Saad Jbabdi [mailto:[log in to unmask]]
Sent: Wednesday, August 10, 2011 4:16 AM
To: [log in to unmask]
Subject: Re: [FSL] probtrackx registration
> When running probtrackx using classification targets in standard (MNI) space, is it possible to get the results in diffusion space? In previous runs, I've chosen the 'seed space is not diffusion' option and supplied the 'standard2diff' linear transformation matrix, and have gotten results in standard space (the original space of the ROIs). However, I would like to visually verify the results by examining the fdt paths for each subject in fslview. This would require the probtrackx results to be in diffusion space. If this is not an option, given masks in standard space, how can I be confident that the registrations from standard to diffusion space worked adequately for every subject?
You can check the registration using a single image (e.g. FA versus T1 versus MNI152). If you are confident that registration is accurate for all your subjects, then you can provide the transformation to probtrackx and run everything in standard space, which we recommend for multi-subjects comparisons.
> A second issue relates to the following. When registering ROIs from standard to diffusion space, there are interpolation effects that make the ROIs not binary any longer and adjacent ROIs can overlap. I assume that these effects are ignored by protrackx, so if one wanted to make sure that there was no overlap across regions, it would always be better to transform the ROIs to individual space and then do some editing before running the tractography. Could someone please give their experience on this?
You don't need to get your ROIs into diffusion space, just stick to standard space and make sure registration is as accurate.
> Thank you for your help.
> Katie Gambale
> Catherine Gambale, B.S.
> Post-Baccalaureate IRTA
> Genes, Cognition, and Psychosis Program
> Clinical Brain Disorders Branch, NIMH
> 10 Center Dr., Bldg. 10, Room 3C205
> Bethesda, MD 20852
> Phone: (301)-496-9672
> Email: [log in to unmask]
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)