Hi,

There are many review papers in pubmed and even books nowadays  on diffusion MRI and tractography. I would definitely recommend starting with those to get a feeling on what to expect from the data. Regarding your questions:

1. It is difficult to say which version of which software is compatible with different versions of scanner software. We use the latest dcm2nii, which is compatible with different software versions of our Siemens scanners. Best way to tell whether there is anything wrong with your conversion is to use the NIFTI data and extracted bvals and bvecs, fit the tensor model (dtifit) and check dti tensor orientations and diffusivities. 

2. For every diffusion MRI model, information on strength and orientation of diffusion gradients (i.e. bvals and bvecs) is needed. The correction for slice angulation is normally part of the dicom to NIFTI conversion, so no need to worry about that - provided that the conversion has been successful.

3. You can do that on the data file, but this won't take care of bvecs, you need to do that. Again a  simple check of whether everything has worked fine is to fit tensors and look at their principal orientations. If these do not look right (e.g. in the corpus callosum) then you may need to flip one or more dimensions in bvecs vectors.

Hope this helps
Stam

 


On 1 Oct 2013, at 08:58, Blair Johnston wrote:

> Hi, 
> 
> I'm just reposting this message as I haven't received a response.
> 
> "Hi,
> 
> I have worked with structural and functional MRI a lot but I am new to DTI. I was wondering if I could get a little help starting up as I keep finding contradictory information/advice.
> 
> 1. My first question relates to the conversion of images from dicom to nifti format. I have used MRIConvert to transform the DTI data from dicom to FSL NIFTI. This method creates the bval and bvec files as required but an error message states: "Warning: Polarity of the bvecs may be wrong for VB15 data." This issue has been discussed on this forum but the discussions seem contradictory. Some state that the latest version of MRIConvert has corrected this issue for VB15 and others recommend using other software such as the MRICron function dcm2nii.
> 
> 2. On a related note, for my first foray into DTI analysis I only wish to create FA and MD images - does this mean I need to worry about the bvec values? One document I found stated "angulation errors will have little influence on DTI parameters that are invariant to tensor rotation, such as ADC, MD and FA. However, the eigenvectors of the tensor, and consequently tractography programs are sensitive to proper interpretation of the bvecs relative to the imaging plane." however I found a manuscript which states the opposite (http://onlinelibrary.wiley.com/doi/10.1002/mrm.21890/abstract).
> 
> 3. Some of the subject's diffusion images are acquired "upside down". Can FSL flip these images over and are the corresponding bvecs flipped too? I identified the fsl functions "fslreorient2std" and "fslorient" but I'm not sure if that's what I was looking for.
> 
> 4. As I am currently a novice when it comes to DTI, are there any good guides, references or toolboxes that might guide and/or assist me - I'd really appreciate some reliable source of information so I have the confidence that what I am doing is correct. I have been looking into the PANDA toolbox but I wasn't sure if it was the main toolbox.
> 
> Any help or advice will be greatly appreciated.
> 
> Kind regards,
> Blair"
>