All right. Using the installer in GUI mode it might be different from what I said. A lot has changed since the last release. Nevertheless you can simply select a reference diffusion-weighted image before starting the simulation. SImply select it in the datamanager in conjunction with the fibers and everything else. Then, the gradient vectors and b-values of this image are used. In the user manual you can find a (hopefully detailed) description of the 2014.10 version of Fiberfox:
http://docs.mitk.org/2014.10/org_mitk_views_fiberfoxview.html#QmitkFiberfoxViewUserManualSignalGeneration
Beware that a HCP style simulation will take quite long. Maybe up to a week.
As mentioned before, you can also use the command line tool of Fiberfox. It takes a fiber bundle and a parameter file as input. There you can manually aedit the gradients.
Does this work for you?
Peter
________________________________
Von: Pehr Wessmark <***@kth.se>
Gesendet: Montag, 13. März 2017 11:49
An: Neher, Peter
Betreff: Re: AW: Re: AW: Fiberfox Customized Gradient Directions
Certainly. Thank you.
I am using:
MITK Diffusion 2014.10.02 (based on MITK 2014.10.00)
ITK 4.5.1, VTK 6.1.0, Qt 4.8.6
Thanks again.
Pehr
--
On 13 March 2017 at 11:25:05 +01:00, Neher, Peter <***@dkfz-heidelberg.de> wrote:
Hi Pehr,
I'm not in the office today, so I can give you a detailed answer tomorrow or on Wednesday. Just a quick question. Are you using the current mitk master or the mitk diffusion installer? If you are using the installer, which version?
Cheers,
Peter
---- Pehr Wessmark schrieb ----
Hi Peter,
Thank you for your suggestion. I am quite new to Fiberfox so I am not up to speed with the different views in the program.
You mentioned that I could use the customized gradients in the GUI by using them as a template. Could you be more specific as to how this is done? I can only find the option that lets the user specify the number of gradients.
As for the command line tool: are you referring to the Command Line Module view in Fiberfox?
Thanks you again.
Sincerely,
Pehr
KTH Royal Institute of Technology,
Stockholm
--
Hi Pehr,
if you are using the GUI, you can set the 90 gradients diffusion-weighted image as "template". Then Fiberfox uses these gradients. If you are using the command line tool, your modified XML parameter file should work fine.
Cheers,
Peter
________________________________
Von: Pehr Wessmark <***@kth.se<mailto:***@kth.se<mailto:***@kth.se>>>
Gesendet: Freitag, 10. März 2017 15:15
An: mitk-***@lists.sourceforge<mailto:mitk-***@lists.sourceforge>.net<mailto:mitk-***@lists.sourceforge.net<mailto:mitk-***@lists.sourceforge.net>>
Betreff: [mitk-users] Fiberfox Customized Gradient Directions
Hi,
I am trying to import 90 gradient directions from the Human Connectome Project into Fiberfox. Trying to edit the saved parameter XML file does not work as Fiberfox overwrites the gradient data.
Is there a way to solve this problem and to customize the gradient directions in Fiberfox?
Thanks in advance.