# Dog brain DTI problems

**URL:** <https://discourse.slicer.org/t/dog-brain-dti-problems/1850>\
**Category:** SlicerDMRI\
**Created:** [January 16, 2018, 3:07am UTC](https://discourse.slicer.org/t/dog-brain-dti-problems/1850 "2018-01-16T03:07:16Z")\
**Posts on this page:** 6\
**Page:** 1

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**Author:** ![opetne](https://avatars.discourse-cdn.com/v4/letter/o/71e660/32.png) [@opetne](https://discourse.slicer.org/u/opetne)\
**Post date:** [January 16, 2018, 3:07am UTC](https://discourse.slicer.org/t/dog-brain-dti-problems/1850/1 "2018-01-16T03:07:16Z")

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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.

Best,

Ors Petnehazy

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**Author:** ![ihnorton](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ihnorton/32/9_2.png) [@ihnorton](https://discourse.slicer.org/u/ihnorton)\
**Post date:** [January 16, 2018, 2:48pm UTC](https://discourse.slicer.org/t/dog-brain-dti-problems/1850/2 "2018-01-16T14:48:13Z")

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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 🐕).

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**Author:** ![opetne](https://avatars.discourse-cdn.com/v4/letter/o/71e660/32.png) [@opetne](https://discourse.slicer.org/u/opetne)\
**Post date:** [January 18, 2018, 10:19am UTC](https://discourse.slicer.org/t/dog-brain-dti-problems/1850/3 "2018-01-18T10:19:32Z")

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> [@ihnorton](#):
>
> inorton -at- bwh dot harvard dot

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,

Ors

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**Author:** ![opetne](https://avatars.discourse-cdn.com/v4/letter/o/71e660/32.png) [@opetne](https://discourse.slicer.org/u/opetne)\
**Post date:** [January 18, 2018, 10:20am UTC](https://discourse.slicer.org/t/dog-brain-dti-problems/1850/4 "2018-01-18T10:20:32Z")

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Dear Isaiah,

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

Best,

Ors

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**Author:** ![ihnorton](https://sea2.discourse-cdn.com/flex002/user_avatar/discourse.slicer.org/ihnorton/32/9_2.png) [@ihnorton](https://discourse.slicer.org/u/ihnorton)\
**Post date:** [January 19, 2018, 5:29pm UTC](https://discourse.slicer.org/t/dog-brain-dti-problems/1850/5 "2018-01-19T17:29:52Z")

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@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](http://dmri.slicer.org/docs/)).

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:

 ![image](https://us1.discourse-cdn.com/flex002/uploads/slicer/original/3X/6/f/6f823a9c2f8b8569cc2a9656e56da92a37919262.jpeg)

Regarding

> 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.

Best,  
Isaiah

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**Author:** ![opetne](https://avatars.discourse-cdn.com/v4/letter/o/71e660/32.png) [@opetne](https://discourse.slicer.org/u/opetne)\
**Post date:** [January 19, 2018, 6:19pm UTC](https://discourse.slicer.org/t/dog-brain-dti-problems/1850/6 "2018-01-19T18:19:51Z")

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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.

Best,

Ors

Isaiah Norton [slicer@discoursemail.com](mailto:slicer@discoursemail.com) (időpont: 2018. jan. 19., P,  
18:39) ezt írta: