Hi Philipp,
- Here comes my first question: Would it be possible to define own
gradient direction? On the website, you write that the parameters can be
changed according to the MR sequence-parameters, but I don't find any option to
change the gradient directions, only the number of directions seems to be
selectable?
The direction cannot be specified from the GUI, however a typical
diffusion-weighted image stored in the NRRD format ( *.dwi - there are several
such images in the DiffusionTestData.zip archive ) contains of a
meta-information about the gradients similar to the following
DWMRI_b-value:=200.000000
DWMRI_gradient_0000:=0.000000 0.000000 0.000000
DWMRI_gradient_0001:=0.500000 0.500000 0.500000
DWMRI_gradient_0002:=0.000000 0.000000 0.000000
These come from an IVIM dataset with isotropic direction. The specified b-value
is a reference value and the b-vaules of the gradient images are derived from
the magnitude of the gradient direction vector. More details can be found here:
http://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:Nrrd_format#Describing_DWIs_with_different_b-values
So if you want to specify the directions you have to fill the gradient meta
information, the easiest would be to take the generated image ( saved in .hdwi
format ) and then modify the header file in an text editor.
This also is related to your second question:
- It would be great if you could give me hint how I could save a whole
artificial diffusion dataset?
You have to specify some diffusion format ( .dwi, .hdwi, .fslgz ) when saving a
diffusion image. Otherwise the writer interprets it as a 3D+t image and so it
is stored. But it is always a single file on the disk.
Best,
Jan
From: Philipp Stämpfli [mailto:[email protected]]
Sent: Montag, 1. Dezember 2014 10:55
To: [email protected]
Cc: [email protected]
Subject: [mitk-users] How to save all volumes of an artificial diffusion dataset
Hello
I try to create an artificial diffusion dataset with MITK. Therefore, I do the
following steps in MITK diffuison:
-On the Fiberfox-Tab, I go to Signal generation and press Start Simulation
- On the Fiber definition Tab, I define two fiber bundles
- I select these two fiber bundles in the "data-manager window" and then click
on "join bundles" on the fiber definition tab
- In the signal generation tab, I select the different parameters and also the
Save-Path-Directory
- Here comes my first question: Would it be possible to define own gradient
direction? On the website, you write that the parameters can be changed
according to the MR sequence-parameters, but I don't find any option to change
the gradient directions, only the number of directions seems to be selectable?
- Finally, I click on Start simulation again... Now, I'd like to save my B0
image and the 30 (or whatever number of diffusion direction) as nii volumes (or
analyze or...), but when I click on the created
Bundle_1+Bundle_0..._StickBall_RELAX entry, only a single volume is saved...
It would be great if you could give me hint how I could save a whole artificial
diffusion dataset? Thank you very much for your help and support!
Kind regards
Philipp Stämpfli
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