[Camino-users] PICo parameters

[Curci Marina Carmela]

Good morning,

I continue to have problems with PICo tractography on DTI data set.
I've tried also to change parameters (lrange, step, model pdf) on the LUT but I don't see a lot of improvements on the final output. I will attach you 2 pictures: one is the probability map in which the seedfile ROI is the brain stem (probmap_default_acm_sc.nii.gz) and one is the probability map in which the seedfile ROI is the precentral region (probmap51_default_acm_sc.nii.gz).
The model for the pdf is a bingham function, lrange is 1-10 and the step 0.02 as the default conditions. SNR is 30.
Could you give your opinion about them please?

I've read that I can use the command pdview to view the outputs of picopdfs and I've tried to see them:

pdview -inputfile pdf_default.Bdouble -inputmodel pico -e1 -pdf bingham -datadims 96 96 34

For each pixel I see 3 different values. Are they the 3 components of the major eigenvalue? Then in brackets I have another number that is the sum of the absolute value of the concentration parameters in the voxel.
How can I check from this last value if my lut is good or not? Will it be more probable that a track will cross voxels where this value is higher? Which parameter most influence this value?

And finally the last question: I run the track command using white matter mask as a background mask, but I see from the output that the background mask is not considered during the tracking. Why does this happen?

Waiting for your answers,
I thank you,
Marina

________________________________________
Da: Curci Marina Carmela
Inviato: sabato 9 giugno 2012 9.01
A: camino-users at www.nitrc.org
Oggetto: PICo parameters

Good morning, I need a suggestion!

I have to do PICo probabilistic tractography on a DTI reconstructed data-set. Seeds are placed in a ROI involving the brain stem. I run the command track and then procstreamlines as reported below:

track -inputfile picopdf.Bdouble -inputmodel pico -header DTI.nii.gz -seedfile normROI83.nii.gz -iterations 5000 - curvethresh 90 -bgmask brain_mask.nii.gz -outputfile tracks83.Bfloat

procstreamlines -inputfile tracks83.Bfloat -outputacm -mintractlength 8 -seedfile normROI83.nii.gz -iterations 5000 -resamplestepsize 0.25 -outputroot probmapROI83

The resulting probability map is not so good in my opinion, because I expect that fibers start from the brain stem and they grow up in a fan-shaped way. Instead in my case the fibers go up only in the two main directions.

What do you think about it? Should I change some parameters running these commands? Or should I change something in the look-up table? I choose a Bingham pdf function, as suggested on the man page of dtlutgen.

Waiting for your feedback,
I thank you for your helpfulness,
Marina!