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TOPIC: DTI processing

DTI processing 9 years 10 months ago #88

  • Ish
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Hi,

I am trying to processes a DWI data, but when I load the the image file and the vectors file noting happens. I am attaching the two files i want to use. The DWI file is a 4d file. I used mricron to convert the dicom to nifti format. My ultimate goal is to do tractography.

I am using the the new version of medInria on a mac 10.6., with 16g of ram and a decent graphic card, but it still seem slow. Is that normal with this software?

thanks.
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Re: DTI processing 9 years 10 months ago #103

  • ocommowick
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Hi,

I have received the data you sent me that goes with it. I tried it on my macbook pro that runs macos 10.6 (only 4g of memory). To me, everything seems to be working fine. By default, the estimation of tensors takes about 30s : medInria indeed computes first a brain mask and then estimates tensors.

Just in case, for us to start on the same basis, the process to estimate tensors is the following :
- drop the 4d image on the dropbox in the right column
- provide the bvec file when asked for it
- click on show tensors or on the scalar image you wish

Here is what I obtain for colored FA.

Hope that helps
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Last Edit: 9 years 10 months ago by ocommowick.
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Re: DTI processing 9 years 10 months ago #104

  • Ish
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Hi,

It works perfectly now(not really sure what I did differently today),and the tractography fiber looks great. thankyou.

One more thing, any advice on ROIs. Should I use a subject's segmented T1 image that is registered to the DTI, or are there template ROIs that I can use.

thankyou
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Re: DTI processing 9 years 10 months ago #105

  • ocommowick
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Well, it's great if it works now :) As for ROIs, the current interface allows you to filter the full brain tractography by delineated ROIs that you import using the bottom part of the diffusion interface. They have to be overlaid on the DTI image.

There exist some white matter atlases in the literature (Catani, ICBM) that could provide you with pre-delineated ROIs. You would need to register them to your image of course.
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