[Camino-users] pico

[Philip A Cook]

Hi, 

A good first step is to look at the PDFs with pdview:

  pdview -inputmodel pico -inputfile brainPICoPDFs.Bdouble -datadims <x> <y> <z>

where x,y,z are the dimensions of your image. Check the orientations and concentration parameters are sensible. The image should resemble an FA image.

The next thing I would do is check the seeds are in the correct place. I usually check this by doing simple tracking first:

  track -inputfile  brainDT.Bdouble -inputmodel dt -seedfile mask | procstreamlines -outputacm -header mask -outputroot dt_streamline_

BTW, you can use the Bayesian tracking algorithm directly with track, skipping the PDF fitting process:

  track -inputfile data.Bfloat -schemefile imaging.scheme -inputmodel bayesdirac_dt -seedfile mask -iterations 100 | procstreamlines -outputacm -header mask -outputroot bayes_



On Mar 4, 2013, at 4:00 AM, Silvia De Santis wrote:

> Hello,
> 
> I am trying to use pico to estimate the probability of connectivity between a bunch of voxels and I get inconsistent results, so I was seeking for help to understand what I am doing wrong. 
> 
> cat brainDT.Bdouble | picopdfs -inputmodel dt -luts picoTable.dat > brainPICoPDFs.Bdouble
> 
> track -inputfile brainPICoPDFs.Bdouble -inputmodel pico -seedfile mask | procstreamlines -outputcp -outputroot results/ -seedfile mask  
>  
> > brainDT.Bdouble is obtained with dtfit and looks ok
> > mask is an indexed mask of voxels (from 1 to n_voxels)
> > picoTable is obtained with dtlutgen
> 
> I get .img files that basically contains white spots that are outside the brain, and since this is the first time I use camino I am really clueless.
> 
> Any kind of help would be greatly appreciated!
> 
> Silvia
> 
> 
> *****************************************************
> Silvia De Santis
> CUBRIC
> School of Psychology
> Cardiff University
> Tel: 029 2087 0354
> Fax: 029 2087 0339
> Web: http://psych.cf.ac.uk/contactsandpeople/researchfellows/desantis.php
> *****************************************************
> 
> 
> 
> *****************************************************
> Silvia De Santis
> CUBRIC
> School of Psychology
> Cardiff University
> Tel: 029 2087 0354
> Fax: 029 2087 0339
> Web: http://psych.cf.ac.uk/contactsandpeople/researchfellows/desantis.php
> *****************************************************
> 
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