[Camino-users] pico

[Silvia De Santis]

> Dear Philip,
> 
> many thanks for your suggestions. PDFs are ok, and so the seeds I think, because if I run track -inputmodel dt I get reasonable results. 
> 
> But as I try this:
> 
> track -inputfile brainDT.Bdouble -schemefile direction.scheme -inputmodel bayesdirac_dt -seedfile mask -iterations 100   | procstreamlines -outputacm -header mask -outputroot bayes_
> 
> I get the error:
> 
> SEVERE: Exception in thread "main" class data.DataSourceException: End of file reached without completing voxel.
> 
> I have the latest software version. Any suggestions?
> 
> Many thanks again,
> 
> Silvia
> 
> 
> 
> On Mar 4, 2013, at 6:37 PM, Philip A Cook wrote:
> 
>> 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
>>> *****************************************************
>>> 
>>> _______________________________________________
>>> Camino-users mailing list
>>> Camino-users at www.nitrc.org
>>> http://www.nitrc.org/mailman/listinfo/camino-users
>> 
> 
> *****************************************************
> 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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