Post edited 2:21 pm – July 15, 2011 by cibuthomas

Thanks Roupeng. That helped with running the HARDi reconstruction without errors.

However the tractography results look very bizarre compared with the tracts extracted with DTI reconstruction ofthe same data. I have uploaded a figure comparing the HARDi vs DTI results. Somehow the gradient table for the HARDi appears to have been corrupted. Is there anyway to set it right? How does DTK know what the bmax is, and does it assume that the first 15 volumes are b0? 

cheers

Cibu

Thanks Roupeng

I am comparing the results of DTI tractography with HARDi tractography. I did the reconstruction in 3 different ways.

1. Using a package called TORTOISE, which does some standard preprocessing routines I get a tensor volume that can be read by Trackvis to do tractography

2. Use Tortoise to do the preprocessing but before doing any tensor fitting I export it in analyze format and then use DTK to do the reconstruction in (a) DTI and (b) HARDi.

The tracts from (1) look consistent with the anatomy. The tracts from 2a and 2b are not consistent with the anatomy, but they are consistent between each other. 

The problem appears to be at the reconstruction end and I am guessing that the gradient table I provide is at the heart of this problem.  I have set b0 to 15 in the UI, but it doesn't change things.

 I was wondering if there is something else I could try like flipping the columns in the matrix etc.

cheers

Cibu

Tracts from a and b loook alike with very  minor differences.

Please note that in the figure below a) represents tracts from DTI recosntruction of the data using DTK, b) represent the same but with HARDI reconstruction.

In contrast the tracts from dti reconstruction of the same data but using a different package look more reliable.

looking forward to your comments

Cibu