As I know, the extension of the MRI is DICOM, and I must convert it to NIfTI. I need to ask about the steps from a scan by MRI machine until the end (can use the image for fiber tracking). I will be grateful if the flowchart has added.
I would suggest you to use FSL. It is one of the best powerful tools to process DTI and medical image in general.
Check the following link where u will find a tutorial how to use in details:
http://www.mccauslandcenter.sc.edu/CRNL/sw/tutorial/html/dti.html
Also, check the following tutorial:
http://www.diffusion-imaging.com/2015/10/dti-tutorial-1-from-scanner-to-tensor.html
If you just need to convert DICOM images I suggest FIJI/ImageJ http://fiji.sc/Fiji
With slicer you can open/convert DICOM images and also do fiber tracking with the respective plugins: https://www.slicer.org/
Both tools are free and open-source
I agree that FSL is a great way to go. We use MRICron or DCM2NII to convert .dcm to .nii files. We use FSL for coregistration and then use the Diffusion Toolkit for final preprocessing before visualizing in TrackVis to do fiber tracking. Have also used 3DSlicer in the past but it's an expensive package.
Agree with Dr Bijanki, this is the exact procedure for processing diffusion tensor imaging
First it is important to have all the acquisitions in DICOM. For conversion to NIfTI it is very easy and fast to use mricron, look for it somewhere. It is free and easy to use. Then with the complete package you can use any software for post processing. FSL is probably the most accessible with free available tutorials, specially if you are looking for adequate probabilistic tractography analysis. Other softwares are available and free like NeuroDebian, however you need Linux so may be yo will need virtual box if you have macOS. Don't know if this will be helpful, just let me know if I can help somehow.
Sorry, I just forgot to say that mricron has 3 icons with different apps, you just use the one called "dcmniigui" (the one with the resonator image ) for conversion
I have documented step-by-step how to process MR data. Have a look here:
jeromemallershandbookofstructuralbrainmrianalysis.yolasite.com/
Jerome
DIffusion DICOMs give the normalized signal at each b-value and each slice. From these you could extract diffusion weighted imaging parameters by fitting functions on them.
- Badges
- Science topic