A few questions

Hi all,

Working with Slicer 4.10.1 and have a few questions:

  1. Is there a way to adjust for eddy current in this (or 4.10.2) version? I have read the FAQ but cannot find the “GTRACT” extension that they mention.

  2. What is the difference between the following tractography modules:

  • Diffusion -> Tratography -> Tractography Seeding; vs
  • Diffusion -> Tractography -> Region-based -> Tractography ROI Seeding; vs
  • Diffusion -> Tractography -> Region-based -> Tractography ROI Selection
  1. Lastly, I have been running DWIconvert fine but for one of my cases DWIConvert either 1) crashes when I use a windows computer; or 2) gives me the following error on the Mac:

Diffusion-weighted DICOM Import (DWIConvert) standard error:
E: DcmElement: CommandField (0000,0100) larger (828667202) than remaining bytes in file

I have not encountered this error before and am not sure how to fix it. Any help would be greatly appreciated.

Many thanks!!


Regarding your questions:

  1. I am not sure if the GTRACT extension is still available. Other options for eddy correction include DTIprep (https://www.nitrc.org/projects/dtiprep), which takes NRRD file as input.

  2. In brief, Tractography Seeding enables multiple options to seed tractography, e.g. from a fiducial. Also, it allows interactive tractography, which means when you move the seeding fiducial, the tractography can be updated interactively.

Tractography ROI Seeding enables only seeding within a predefined mask, usually using a brain mask for whole brain tractography.

Tractography ROI Selection is used for fiber selection using ROIs (a labelmap as defined in Slicer) after you have computed tractography.

Please refer to the Slicer DTI tutorial on the SlicerDMRI documentation page for more information. http://dmri.slicer.org/docs

  1. It’s hard to tell from the error message. I would suggest trying to use the new DCMtNiixGUI module for data conversion, and see if there are still similar problems.


Hi Fan,

Thanks for your response, especially for questions 1 and 2. I will look into DTIprep.

Regarding #3, I tried coverting using dcm2niix v1.0.20190902 - no issues, but when I import this file into Slicer I can’t seem to change the DWI component, etc. I am not sure all the components are there. Do you know if there is a way to check?

Many thanks,

Not sure why I can’t edit my post from yesterday anymore - but exporting the files as .nrrd using dcm2niix seems to have fixed the issue above and I can proceed with my pipeline again.

Thanks for letting us know!