MRtrix3 tractography generation

I am trying to generate fiber tracts for my dataset.
The tutorial at the below location was easy to follow and I was successful.

However, my project dataset does not have all the “necessary files” mentioned in the above link.
In my dataset, I have a folder named “DKI_tensor_b1000”. Inside the folder, I have 144 dicom files that seems to be the data from every slice of the brain. Excuse me if I am not providing sufficient description about the data, but does anyone know how to generate fiber tracts for the file set I have.

1 Like

Hi Reshma,

Firstly I would suggest taking a look at the BATMAN tutorial: it’s far more up to date than that page, which, as shown in the up-to-date version of that page (see both the version number in the hyperlink and the outdated version warning that appears at the top of the page you linked), is for historical reference and not really intended for use.

For pretty much any such tutorial you will need to convert the raw data you have to conform to the expectations of the tutorial. In this case, you don’t want to access the individual .dcm files; instead, MRtrix3 will interpret that directory as an image from which to read. So, for instance, you can use mrconvert with “DKI_tensor_b1000/” as the input, and save the image with any name / format you choose.


1 Like