Connectome for DTI

Issues related to Gradient Tables of DTI

You might need to extract the gradient tables of DTI dataset by hand, instead of the provided used by Diffusion Toolkit.

1. Install mricron which includes the dcm2nii tool.

   cd project/subject/timepoint/RAWDATA/DTI

   dcm2nii *.dcm

2. Use Ipython and Numpy to change the format of the gradient table to fit for DTK.

   ipython

   import numpy as np

   a=np.load('.....bvec')

   a=a.T # transpose

   a = a[5:, :] # need to cut the vectors for b0 volumes (here 5 b0 volumes)

   np.savetxt('customgradienttable.txt', a)

3. No, you can provide your custom gradient table in the "Reconstruction step" of Connectome Mapper