Post edited 4:42 pm – July 19, 2010 by dleve123

To whomever can help:

I am currently in the process of processing and visualizing some DTI (or possibly HARDI) data.  This data has already been processed once through AFNI's DTI processing stream, and the data itself appears to be high quality.  However, I wasn't very happy with AFNI's tractography software and TrackVis seems to be more than adequate, albeit the following issues.

Firstly, it is not clear whether the data should be processed as HARDI or DTI data.  When DT (Diffusion Toolkit) accesses the raw data files, the description field reads hardi, but when part of the data is processed as both HARDI and then as DTI data, the DTI looks significantly better (images later in post)…..

As you can see from the image above, each full acquisition of data is broken up into 4 scans.  Scans 2,3,4 (series 7,8,9) each use 14 gradients and scan 1 (series 6) uses 13 gradients + 1 b0 gradient.  This makes a total of 56 gradients used (including 1 b0 gradient….so 55 oblique gradients).  If each scan has 1008 raw data files, then there are 72 axial slices per gradient, as well as 72 b0 slices.  After much work, I was able to process and visualize the first scan (the scan that includes the b0 volumes or slices) as both HARDI and DTI data….the HARDI processing stream took 12 minutes while the DTI processing stream took 2.  Here is what both the output .trk files look like. HARDIDTI

When I try to process the other scans, I receive cannot read .nii errors (at the _recon stage), which appear to be issues with the gradient file.

I guess my questions are:  Should this data be processed as DTI data (that is my inclination)?  How do I process the other 3 scans without the bO volumes and concatenate them (presumably with track_merge)?  Any other suggestions not explicitly asked for will be more than welcomed.

Thanks,

Daniel