On Jul 3, 2018, at 10:09 AM, Matthew Webster <[log in to unmask]> wrote:

Hi,

    It’s not clear to me at which point in the pipeline below you are registering the FA images to the T1. However if you’re otherwise happy with the output from TBSS you could isotropically resample to 2mm space with ( e.g. ) flirt.

Kind Regards

Matthew

--------------------------------
Dr Matthew Webster
FMRIB Centre 
John Radcliffe Hospital
University of Oxford

On 2 Jul 2018, at 20:39, Dawn Jensen <[log in to unmask]> wrote:

I'm trying to run a fusion analysis on DTI-FA images and T1.  I'm having trouble with the DTI looking off centered and was wondering if I missed a step in the pre-processing.  Below are the DTI processing steps I've taken so far:

1)dicom - nii conversion
2) eddy correct
3) BET extraction
4) DTIFIT
5) fsl_susan to smooth the FA image

The resultant pICA shows all the DTI data shifted high (partially outside the skull at times, but grouped appropriately) and slightly right of center.

My past experience has only been with TBSS analysis, where the images are registered during the process.  As I understand it, TBSS registers them to a 1x1x1 space, and we'd like to keep the images in 2x2x2.  If there's a way to change that part of TBSS registration, I could use that and then fslsplit the all_FA file.  Should I run flirt instead?

Thanks in advance!!

Dawn Jensen
Undergraduate Research Assistant
Brains and Behavior Fellow
Georgia State University

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