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TOPIC: Gradient file

Gradient file 4 years 6 months ago #835

  • ann.bee
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Hi
I recently downloaded the 2.2.2 version of your software and I have tried your sample dataset everything worked out fine.
However when I try DTI estimation with my DWI data it aks for the "gradient file". I've tried with your "gradient7.txt" file but nothing happened, i get the error: "mismatch between image lenght (6) and image dimention (2). how can I get the .txt file? if you could help me with this I'd really appreciate it

thank you in advance
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Gradient file 4 years 6 months ago #836

  • ocommowick
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Hi,

medInria assumes your diffusion data to be made of two files :

- a single 4D image containing a series of diffusion weighted images
- a text file containing the list of gradients that were applied during the acquisition to obtain the images.

This text file is what you are missing. I would say you have two solutions to obtain it. If you are using a dicom converter to convert your data (like dcm2nii), it usually outputs a .bvec file when it converts diffusion data. If that is the case, you can directly use that .bvec file inside medInria. Otherwise, these gradients are usually available in the protocol you used at your MR scanner. You could then just stack them into a text file (just like the gradient7.txt in our example).

Hope this helps
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Gradient file 4 years 5 months ago #838

  • ann.bee
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Hi. Thanks for your help i've tried everything that you told me but still can't estimate the tensors. I get the message "operation failed" even with the .bvec file.
what else could be happening?
how many gradients directions at least needs to have my data?
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