Fork me on GitHub
Welcome, Guest
Username: Password: Remember me

TOPIC: Tensors estimation

Tensors estimation 10 years 1 month ago #31

  • Thibault
  • Thibault's Avatar
Hi everybody,

I'm working on a DTI project and my first step is to estimate the tensors of dicom (.dcm) images. I have 169 images for each patient: (1 image for b = 0 , 12 images for 12 directions of gradient with b = 700) X 13 (Nex).
First i used to convert dicom files to nifti, i put the .nii file for tensors visualisation and i attached the corresponding bvec file for the gradient. This worked great, I could see the tensors for the different eigenvalues.
Now i want to use medInria in command line for analysing a large volume of images. Is it possible ? ( i use medInria on Windows 8 ).

Regards,
The administrator has disabled public write access.

Re: Tensors estimation 10 years 1 month ago #32

  • bbleuze
  • bbleuze's Avatar
  • OFFLINE
  • Administrator
  • Posts: 5
  • Thank you received: 1
  • Karma: 1
Hi Thibault,
Unfortunately there is no command line interface for medInria 2 yet. We've had that question several times already and are probavbly going to integrate something along the lines of either command line interface or scripting interface (like python wrapping).
Ben.
The administrator has disabled public write access.
The following user(s) said Thank You: Thibault

Re: Tensors estimation 10 years 1 month ago #35

  • Thibault
  • Thibault's Avatar
Hi again,

I have another question : should i obligatory run tractography to estimate diffusion tensors from my nifti file? I need ADC and FA values . So i click on show tensors and then i click on Coloured FA map. I obtain my FA map for my 20 different slices but i don't know at witch values correspond the differents colours.
Can somebody explain this please?

Regards,
The administrator has disabled public write access.

Re: Tensors estimation 10 years 1 month ago #36

  • Thibault
  • Thibault's Avatar
I attach a screenshot of what i mean.

regards,
ColorFA.JPG
The administrator has disabled public write access.

Re: Tensors estimation 10 years 1 month ago #41

  • smedina
  • smedina's Avatar
  • OFFLINE
  • Administrator
  • Posts: 15
  • Thank you received: 2
  • Karma: 1
Hi Thibault,

Voici the explanation:

FA pixels are colorized in relation with the principal direction of diffusion (i.e. principal eigenvector of the tensor). Consequently, the color represents an indication of the direction of the fiber bundles. A red pixel indicates that in this location white matter is mainly orientated Left-Right. Anterior-Posterior orientation is indicated by a green pixel and Inferior-Superior orientation by a blue one.

Hope this helps!

serch.-
The administrator has disabled public write access.
The following user(s) said Thank You: Thibault

Re: Tensors estimation 10 years 1 month ago #42

  • Thibault
  • Thibault's Avatar
Hi,
Thanks for your answer :)
I have a last question: i'm trying to extract informations about tensors with matlab.
How are saved the tensors in vectors in nifti files? Is it the upper triangular matrix (Dxx, Dxy, Dxz, Dyy, Dyz, Dzz) or the lower (Dxx, Dyx, Dyy, Dzx, Dzy, Dzz)?
Thank you ! :)
The administrator has disabled public write access.

Re: Tensors estimation 10 years 4 weeks ago #44

  • ocommowick
  • ocommowick's Avatar
  • OFFLINE
  • Administrator
  • Posts: 49
  • Thank you received: 5
  • Karma: 7
Hi,

Just in case you hadn't found it by yourself in the meantime. When you export the tensors, it is the lower triangle of the tensor that is written : (Dxx, Dyx, Dyy, Dzx, Dzy, Dzz).

Hope that still helps.
The administrator has disabled public write access.
Time to create page: 0.119 seconds