Diffusion Processing Pipeline/bugs and feature requests

Bugs

mrifilt3, mricrop, mrisubset, and possibly others mangle the parameters file. In particular, if you operate on a DWI, the output won't have the b matrix recorded. Also the MRISpaceShift just gets clobbered to 0 0 0.
- A workaround right now for the b matrix, TR, and TE is
```
grep "^b\|e0" $src/parameters >> $dest/parameters
```
Streamtube generation gets slower and slower as the program runs. What's going on? Is it running out of memory, reading inefficiently through a big file, doing something probabilistic that gets less likely the more tubes there are? We need a speedup!
- In tubegen, unless the argument -cd 0.0 is passed to turn off inter-curve distance-based culling, an O(n²) culling step happens --- O(k) after tube #k has been generated. It would be a good idea to separate out seeding, streamline/tube generation, and culling, since each of these can be modified or optimized separately. There's a lot of code repetition in streamtube.cpp. --- Jadrian Miles 14:04, 24 March 2009 (UTC)
- See Tubegen/bugs and feature requests for more notes.

Most operations, including tensor fitting and tube generation, are highly parallelizable. It'd be great if we could throw them on the department's compute grid.
Rename batch scripts to get rid of ambiguous terms like "process". processNiftiDwis.py, for example, could be changed to nifti2mriimage_batch.py.