Diffusion Processing Pipeline/bugs and feature requests: Difference between revisions
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* <tt>mrifilt3</tt>, <tt>mricrop</tt>, <tt>mrisubset</tt>, 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 <tt>MRISpaceShift</tt> just gets clobbered to 0 0 0. | == Bugs == | ||
* <tt>mrifilt3</tt>, <tt>mricrop</tt>, <tt>mrisubset</tt>, 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 <tt>MRISpaceShift</tt> just gets clobbered to 0 0 0. | |||
** A workaround right now for the b matrix, TR, and TE is <pre>grep "^b\|e0" $src/parameters >> $dest/parameters</pre> | |||
* 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! | * 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 <code>-cd 0.0</code> is passed to turn off inter-curve distance-based culling, an O(n<sup>2</sup>) 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 <tt>streamtube.cpp</tt>. --- [[User:Jadrian Miles|Jadrian Miles]] 14:04, 24 March 2009 (UTC) | |||
** See [[Tubegen/bugs and feature requests]] for more notes. | |||
== Feature Requests == | |||
* 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". <tt>processNiftiDwis.py</tt>, for example, could be changed to <tt>nifti2mriimage_batch.py</tt>. | |||
[[Category:Diffusion MRI]][[Category:Bug Tracking Pages]] | [[Category:Diffusion MRI]][[Category:Bug Tracking Pages]] | ||
Latest revision as of 14:22, 24 March 2009
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
- A workaround right now for the b matrix, TR, and TE is
- 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 0.0is 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.
- In tubegen, unless the argument
Feature Requests
- 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.