[Mrtrix-discussion] nii conversion and general questions

[Kerstin Pannek]

Hi all!
Thanks for the new release! This will make my life a whole lot easier!

I just have a few quick questions:

1) I noticed that the transformation in the header file when converting 
from *.nii is not identity any more (as is used to be when converting 
from ANALYZE). I assume I can therefore not use the bvecs I use for 
FSL-analysis? Would I get the gradient scheme directly from DICOM then? 
On the other hand, if I would use mrconvert to convert from *.mih to 
*.nii, could I then use the *.mih gradient scheme for FSL-analysis? Or 
do I need 2 sets of bvecs, one for mrtrix, one for FSL?

2) During CSD computation, I sometimes get a message "csdeconv: failed 
to converge". Should I be worried about that and reduce lmax? The 
computation continues after this message, and the results look 
reasonable to me. My dataset is 65 directions, b3000, 2 averages, lmax 
8. This is the command I ran:

$ csdeconv ../data/data.mih -grad ../data/encoding.b -lmax 8 
response.txt -mask ../data/nodif_brain_mask.mih CSD8.mih

csdeconv: performing constrained spherical deconvolution...  
63%csdeconv: failed to converge
csdeconv: performing constrained spherical deconvolution... 100%

3) Is it possible to extract the fibre orientation and fraction 
information from the CSD-file?

Thanks
Kerstin