Hi Arnaud,
1. I do not see anything wrong with the output. Do you happen to have data you can share that shows this error? 2. Just a quick check. Did you just press the “Start simulation” button without selecting a fiber bundle in the data manager? In that case a dummy 3D image is generated which can then be used to create fibers in the “Fiber Definition” tab. You can also check whether the “Fiber Bundle: ” label in the Data box reads anything other than “mandatory”. [1] Best, Caspar [1] http://docs.mitk.org/nightly/org_mitk_views_fiberfoxview.html Von: Arnaud Boré [mailto:[email protected]] Gesendet: Mittwoch, 19. August 2015 15:38 An: Goch, Caspar Jonas Cc: [email protected] Betreff: Re: [mitk-users] [MITK DI] Hi Caspar, 2015-08-19 6:43 GMT-04:00 Goch, Caspar Jonas <[email protected]<mailto:[email protected]>>: Hi Arnaud, 1. Is there any error output in the logging view? Can you save the images correctly as .dwi? (.dwi is a renamed nrrd file and contains the gradient information in the header) Yes I'm able to save and then load correctly a .dwi file but when I try to save it as nifti file I get this log file Info BlueBerry mbilog backend registered BlueBerry Info Logfile: /home/borear/.local/share/data/DKFZ/MitkDiffusion_202313406/data/13/mitk-0.log Info **** Activating legacy standalone functionality Info setting active flag Info BlueBerry Workbench ready BlueBerry Info **** Activating legacy standalone functionality Info setting active flag Info ** Changing locale from en_CA.UTF-8 to 'C' Info GDCM 2.4.1 used for DICOM parsing and sorting! Info Current memory usage: 2.80 GB (8.95 %) Info ... found 65 different files Info Retrieved 1outputs. diffusion.dicomreader Info Output 1 Got vendor: SIEMENS image type ORIGINAL\PRIMARY\DIFFUSION\NONE\ND\MOSAIC diffusion.dicomreader Info -- Analyzing: /home/borear/Downloads/ERANET_EN464_2/09-DTI_64_Saad/ERANET_EN464_2-0001.dcm #######.... (I didn't put everything here) Info -- Analyzing: /home/borear/Downloads/ERANET_EN464_2/09-DTI_64_Saad/ERANET_EN464_2-0065.dcm Info ---- DICOM Analysis Report ---- :: Output 1 of 1 diffusion.dicomreader Info :: Analyzed volumes 65 :: 1 b = 0 :: 64 b > 0 Info =========================================== diffusion.dicomreader Info -- Analyzing: /home/borear/Downloads/ERANET_EN464_2/09-DTI_64_Saad/ERANET_EN464_2-0001.dcm Info == MOSAIC: ImageRegion (0x7fffda6795e0) Dimension: 3 Index: [0, 0, 0] Size: [864, 864, 1] Info ======== Loading volume 1 of 65 #######.... (I didn't put everything here) Info ======== Loading volume 65 of 65 Info Diffusion-Image successfully initialized. Info Timing information Info ** Changing locale back from C to 'en_CA.UTF-8' Info Finished import with memory: Info Current memory usage: 2.88 GB (9.20 %) Info **** Activating legacy standalone functionality Info setting active flag Info Writing image: /home/borear/Desktop/DTI_64_Saad_9_ERANET_EN464_2.nii Info Could not reset locale ��� ________________________________ 2. If you generate a diffusion weighted image with the signal generation and save it as either .nii or .dwi the used gradients will be saved alongside (in bvecs/bvals or the header respectively) When I create a "dummy" using signal generation with 30 directions (by default) I get a 3D volume not a 4D image. I'm not able to go through what you call channels. Best, Caspar Von: Arnaud Boré [mailto:[email protected]<mailto:[email protected]>] Gesendet: Mittwoch, 19. August 2015 00:54 An: [email protected]<mailto:[email protected]> Betreff: [mitk-users] [MITK DI] Dear MITK experts, I've got a couple of questions regarding MITK Diffusion. 1 - When I import a dicom folder and then I try to save the result as a NIFTI file the progress bar stays at 50% and I'm not able to open the file that has been created. I would like as well to extract gradient information (like a bvec bval or .b - mrtrix version), how do I do that ? 2 - When I use signal generation with a specific number of gradients where can I found this table ? I try to generate a phantom and run some analyses outside MITK so I would like to create a 4D nifti file and a gradient table. Thank you in advance for your help. -- Arnaud BORE Research assistant Cellulaire : (001) 514-647-8649
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