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"
|