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TOPIC: vector file load for DTI stack

vector file load for DTI stack 9 years 10 months ago #106

  • arvid
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Hi,
Thanks for a wonderful software! I'm a new user, but it seems extremely powerful.
I have a really exciting exvivo DTI dataset from a 9.4T scanner just waiting to be analyzed, but I can't get the diffusion workspace to do what I want..
I've managed to load the images so that I can view the T2 anatomy (through DICOM), but I can't get the FA maps. I've also tried the example file (med.inria.fr/images/downloads/xDTICUBE-4D.zip) and it presents identically as my data:

1) I find the "patient" under visualization, and every slice presents with a timeline, where every time point seems to be corresponding to a diffusion vector (number of time points coincide with number of vectors)
2) When I switch to diffusion, I only see the T2 anatomy, and no FA maps. No matter what I try..

I realized I never got the option to load the vector.txt file, the software never asked for it - is that why it's not working?
I'm using MedINRIA 2.0.1 under OS X 10.6.8 on a 2.66Ghz MBP, 4GB DDR3.

Any suggestions greatly appreciated!!

/Arvid
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Re: vector file load for DTI stack 9 years 10 months ago #107

  • Ish
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Hey Arvid,

I would recommend that you first convert your dicom images to 4D nifti(I use the mricron for this). Then load 4D and it should ask for the vector file.

Ish
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Re: vector file load for DTI stack 9 years 10 months ago #108

  • arvid
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Thanks for quick reply! I didn't try that because I got the impression that you could load DICOMs directly in the new version, also the example file for diffusion shows up identically as my DICOMs when I load them directly..
Anyway, will try mricron - if anyone knows a way of using DICOMs directly please post!
All the best
Arvid
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Re: vector file load for DTI stack 9 years 10 months ago #109

  • arvid
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Hmm, tried MRIcron, when I process my data through it I seem to end up with only the T2 stack, none of the vectors..
to be continued :)
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Re: vector file load for DTI stack 9 years 10 months ago #110

  • ocommowick
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Hi,

A lot to answer here. There is dicom conversion included in medInria. With a DWI dataset, you should obtain one 4D image. When you get to visualization and view that image, you indeed see the first volume by default. You can then view the diffusion volumes by using the time management toolbox.

Now, if you want to use this volume in the diffusion workspace, you also need the diffusion gradients. I don't remember if medinria is outputting it too automatically. Otherwise, mricron should be outputting a bvec file with the 4d volume.

To use all this, drop the 4d image in the drop box in the right column (after choosing dti track in the menu). Then medInria will ask you for the bvec file and you can compute FA or DTI.

Hope that helps
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Re: vector file load for DTI stack 9 years 10 months ago #111

  • arvid
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Thank you! This is so funny, I've been doing everything right, just not drag/dropping the file in the right box :)
Anyway, summary:
Importing the DICOMs directly from the scanner works perfect!
Thanks again!
/arvid
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