Hi Marcella, you have three different options to load diffusion weighted datasets.
1) dicom import of Siemens files If you choose one of the following two options, you have to change the file-endings. If you don't do that, MITK will not be able to differentiate them form plain 4D-images. After loading, you will recognize the different icon used for diffusion images, compared to plain 4D images: 2) use the nrrd-format, like Slicer does first rename *.nhdr => *.hdwi *.nrrd => *.dwi 3) use the nifti-format, like FSL does first rename *.nii => *.fsl *.nii.gz => *.fslgz For option 2), the nrrd-header should include DWMRI_b-value, DWMRI_gradient_xxxx, measurement frame, modality:=DWMRI, as in the following example: NRRD0004 type: short dimension: 4 space: left-posterior-superior sizes: 7 32 66 20 space directions: none (1,0,0) (0,1,0) (0,0,1) kinds: vector domain domain domain endian: little encoding: raw space origin: (0,0,0) data file: data.raw DWMRI_b-value:=1000.000000 DWMRI_gradient_0000:=0.000000 0.000000 0.000000 DWMRI_gradient_0001:=0.710300 0.000708 -0.703899 DWMRI_gradient_0002:=-0.710300 0.000708 -0.703899 DWMRI_gradient_0003:=0.002857 -0.708531 -0.705674 DWMRI_gradient_0004:=0.002856 -0.708174 0.706032 DWMRI_gradient_0005:=0.708873 -0.705331 -0.002833 DWMRI_gradient_0006:=-0.708873 -0.705331 -0.002833 measurement frame:=(1.000000,0.000000,0.000000) (0.000000,1.000000,0.000000) (0.000000,0.000000,1.000000) modality:=DWMRI For option 3), the *.fsl (or *.fslgz) file must be accompanied with a bvals and a bvecs file for the b-matrix information: diffusionimage.fsl diffusionimage.fsl.bvals diffusionimage.fsl.bvecs with the bvals-file containing 0 1000 1000 1000 1000 1000 1000 and the bvecs-file containing 0 0.7103 -0.7103 0.002857 0.002856 0.708873 -0.708873 0 0.000708 0.000708 -0.708531 -0.708174 -0.705331 -0.705331 0 -0.703899 -0.703899 -0.705674 0.706032 -0.002833 -0.002833 using the same example as in 2). Hope, this helps! Regards Klaus ________________________________________ Von: Marcella Laganà [[email protected]] Gesendet: Dienstag, 15. November 2011 22:17 An: Fritzsche, Klaus H. Betreff: R: about MITK Diffusion Thank you for your fast answer. This software seems very comprehensive, I've read the documentation but I'm not able to start using it. I've tried again loading dicom, or different 3D volumes, or 1 4D volume (fsl output). I've also tried creating a 4D volume which is composed by only 1 b0 and 12 directions, so that I've selected the option of 12 directions. I've clicked on Tensors and then on the dataset, but the ITK tensor reconstruction didn't become active (attached the screenshot). Is it the same to load separate 3D files or 4D or dicom? Don't I have to insert the B-matrix? Thanks and regards Maria Marcella Laganà ------------------------------------------------------------------------------ RSA(R) Conference 2012 Save $700 by Nov 18 Register now http://p.sf.net/sfu/rsa-sfdev2dev1 _______________________________________________ mitk-users mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/mitk-users
