Hi Martin,

I am using a macOS Sierra and have DTIPrep as a standalone program.

I actually tried to add it as an extension in Slicer (version 4.6.2) but could not figure out the steps to do that. Do you know how to add it as an extension in that version or an older version? Or, is it best to use the standalone program? 

Also, after I ran the DTI protocol it does create  the QC results and new nrrd image but I cannot figure out how to convert it into a NIFTI format to then use in FSL. I receive an error "The only supported output type is . You may consider using allowLossyConversion option.However, use this option with caution! Conversion from images of a different type may cause data loss due to rounding or truncation." I tried running with allowing LossyConversion but it only saves a bvec and bval file but no NIFTI image. I am unsure if the issue I am having converting the image to FSL format is due to an issue within Slicer or because of the errors i am receiving using the DTIPrep. 

One other question, when I try to view the output to do the visual checking, i click on the 3D viewer mode but do not see a sphere with the distribution of direction of gradients that the manual talks about, it is just a grey screen. 


Any help on these steps would be much appreciated. I've been trying to go off the 'Quality Control Tutorial for DTI' but I am new to this pipeline and am not entirely sure I am doing it correctly. 

Thanks,

Megan