Dog brain DTI problems

Dear Users,

My name is Ors Petnehazy and I’m interested in 3D veterinary anatomical reconstrucions. I know some features of the Slicer. I made some reconstructions already (air sacs, horse stifle CT, MR, etc.).
For a research project I need to reconstruct a dog brain DTI series. I followed the instructions I found made by Sonja Pujol with my own dataset. After some step I only get a dark “image” as a result. I’d like to ask for your help for DTI reconstruction of a dog brain DTI dataset.


Ors Petnehazy

Hi Ors,

Welcome to the forum. Could you clarify your workflow please?

  • What Slicer version? What operating system?
  • What scanner did you use to scan?
  • Do you have DICOM images, and are you converting with DWIConvert? or some other steps?
  • Which step is run before you get the dark image?

It may also be helpful if you can share the data, either converted or raw DICOM, using dropbox/onedrive/etc. If you prefer to share privately please email the download link to me at inorton -at- bwh dot harvard dot edu. (hopefully there should not be any confidentiality issues :dog:).

I followed the steps again, written in the DiffusionMRIanalysis PDF. I attach the screen savings I made during the procedure.
First, I’m not familiar with the DTI procedure, I understood only the basics but I try to do my best to improve in it.
The dataset comes from a 3T Biograph (Siemens). I tried to find any information about the resulting files of the DTI measurement but I was not sure what dataset I have to open for the reconstrucions. I tried all of these for doing the DICOM to NRRD transformation but there was only one where the transformation was successfull. So I worked with this dataset.
It was interesting that after each step when I changed the view from trans (red) to sagittal (yellow) for example the blue brain mask was on the new orientation. After making the brain mask, I saw that it contains the temporal muscles and the whole head as well… I was sure after this stpe that there is something not working properly…

I send you the dataset and the screen captures via wetransfer.

Kind regards,


Dear Isaiah,

Thank you for your offer. I wrote my impressions in a separate message.



@opetne thanks for sharing the data. The first dataset ep2d_diff_mddw_64_p2 seems quite distorted and I didn’t get good results from it.

The second dataset ep2d_diff_mddw_64_p2_4100_tra looks pretty good. I recognize the major structures anyway (I don’t know anything about canine neuroanatomy!). I followed these steps:

  • DWIConvert
  • Diffusion Brain Masking
  • Diffusion Tensor Estimation
  • Tractography Seeding module (see the “Slicer Neurosurgical Planning Tutorial” linked here).

From your screenshots, I think you did the same except the last step.

The resulting tracts seem ok (again with no specific knowledge). Here is a screenshot:



It was interesting that after each step when I changed the view from trans (red) to sagittal (yellow) for example the blue brain mask was on the new orientation.

I think you may have several datasets open? They have different image sizes, so it could lead to some confusion. Also, you should use the DWI volume ep2d_diff_mddw_64_p2_4100_tra in Slicer. The other ones with e.g. _TR or _FA in the name are calculated on the scanner, and there seems to be some change in the orientation/origin so the images are not directly comparable.

Your screenshots look good so far, except the mask overlay issue. So, I suggest to work with your dataset ep2d_diff_mddw_64_p2_4100_tra, and also try some of the example tutorial data from the link above to learn more processing steps. If you have any more questions, please let us know.


Dear Isaiah,

Thank you so much for this explanation. You are right the images seem
distorted for me too, at the beginning I was wondering if there will be any
useable results from this dataset.
For my trials i was using only one dataset, I have to check which one it
was but I guess it could comprise more image orientation.
I’ll go trough the steps again and hopefully I can have better results.



Isaiah Norton (időpont: 2018. jan. 19., P,
18:39) ezt írta: