DWI to DTI Estimation Problem

Operating system: Win 10 Pro
Slicer version: 4.5.0-1

Hello everyone,

I want DWI images convert to DTI and tractography. First step, i created .nrrd file, baseline and mask. Later, DWI to DTI estimation module is working but i can’t see DTI images. The screen is seeming black blank. How can I fix the problem?


To get started, download the latest nightly version of Slicer and install the SlicerDMRI extension.

Thank you for quick response. I setup 4.7.0-2017-07-18 version and installed DMRI extension. I got error message:

Diffusion Brain Masking standard error:

C:/Users/mehme/AppData/Roaming/NA-MIC/Extensions-26156/SlicerDMRI/lib/Slicer-4.7/cli-modules/DiffusionWeightedVolumeMasking.exe: Error parsing Diffusion information, no B0 images

What are your B-values? The default maximum B-value is 100 in order to be considered a B0, but that can be changed under the Mask Settings:

My B-values are automatic 100 in mask settings. As if i change baseline B-value threshold parameter, i got error message. How i can learn B-values? I want my DWI images analyses for tractography so 3D slicer 4.5 and 4.7 nightly version but i got error message or i seen black screen. I tried diffusion MRI tutorial data so i could. But my datas (20 different patients on DWI images) are failed. How can i fix it? I’ve been struggling for 2 weeks.

I think my b-values are 1000.

It is not clear if your dataset has multiple diffusion weighted images or just one image. Please check if your data is in fact a DWI image that is compatible with DTI analysis. In the Volumes module, you should be able to see multiple components in your DWI (multiple diffusion-weighted images from the application of multiple diffusion-sensitizing gradients). Look at Volumes->Volume Information->Number of Scalars. This must be 7 or higher for DTI analysis. Then you can go to Display->Scalar Display to visualize each DWI component.

Thank you for your quick response Lauren. My number of scalars are empty? So i can’t move scalar display bar.

My data images are multiple DWI.

Each of those individual files is relatively small and may only be a single slice each. So this might be the slices for only a single volume. Note that there are other kinds of diffusion scans (or scalar output from the scanner such as ADC maps) which are not compatible with DTI analysis. You could share some (!anonymized!) headers to get feedback, see instructions here:

But probably the best option is to contact whoever is responsible for scanning these images to verify the scanning protocol.

My metadatas:

In addition, when i’m tried, not only 20 patients but also 2 different instution’s patients so 2 different MRI machines but i can’t tractography.

Thank you for your interest Mr. Norton.

These tags look like a trace weighted or ADC map. It appears to not be a DWI from a DTI protocol. I recommend investigating if other images were saved on the scanner and finding out what the acquisition was.

What do you mean other images? If you have dwi images that work for you, can you send me the meta data? According to these parameters, we make our next MRI protocol at least.

Thanks Mrs. Lauren.

This is a trace image:

It looks like you are using the Siemens product sequence, which should work fine, but you need the original DWI images (these derived maps are automatically computed by the scanner by default, but it can be turned off in the protocol card). The raw DWI will have lower series number and the ImageType tag should look like:


(it might not say MOSAIC at the end, but it needs to say ORIGINAL\PRIMARY)

@ihnorton I’ve improved the metadata dialog to be able to filter for specific tags and export all of them in all of the selected patient, study, or series. It is implemented in CTK and waiting for the pull request to be merged (https://github.com/commontk/CTK/pull/728), but it should get into the nightly Slicer version within a few days. That should help figuring out what kind of data the user has much more quickly.

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Thank you very much @ihnorton and @lassoan :slight_smile:
Yes, MRI machine is Siemens’s product. I have also another image series of other institute. ImageType tag is yours said @ihnorton. But i trying again and again, still i can not tractography. Look at this please.
So how can i turned off in the protocol card or whom should i say this situation? Briefly, what can i do?

Hello this is still not a diffusion volume. It does not say diffusion in the ImageType.

In addition to trace and other derived images, the original diffusion DWI should have also been saved on the scanner. It is necessary to talk to the MRI technician, MRI physicist, or look in the image archives to find this image.

OK. Thank you very much for all and advance. In addition I really appreciate for this software :slight_smile:

Best regards,

A. BeriL

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hello,maybe I need your help .I met the same problem.I created .nrrd file, baseline and mask. DWI to DTI estimation module was working and it did not prompt errors but I did not see DTI image(it is black), and I want to know if you solve the problem by finding the original diffusion DWI .Thank you!

Hello, I am working on a new DWI set, de-identified, from a phillips machine. I’m getting 34 directions, a multi volume and a DWI volume showing up in the DICOM viewer. However, in the brain mask step I am getting an error for no b0. How do I work with this error? Happy to share the files as I am somewhat new to this process and could use the guidance.