I have the following questions regarding a few of the procedures introduced in the processing pipeline for the FSL FDT/User Guide.
1. Is the function "topup" essential if our scanning protocol included a field map?
(Data collected used SIEMENS Prisma, with the syngo MR D13D software)
2. When using the "topup" function, how do we specify the "parameters.txt" file for "--datain"? (i.e. where and what parameters do I pull out from the header/description files?)
3. If we do end up using the "topup" function, does that mean there is no need for scanning a field map during our protocol?
4. If we do not use the "topup" function and use the field map directly, how do we specify the parameters for the function "eddy"?
5. Are there any issues with FDT FLIRT registration if the DTI data collected does not cover the whole brain?
Most importantly...
6. How do we convert "probtrackx" output into 3D rendering of fiber bundle projections for visualisation (i.e. similar those published in this paper: http://jov.arvojournals.org/article.aspx?articleid=2121957)?
Thanks!
JJ
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