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Forum Diffusion Toolkit Usage Tensor reconstruction with GE DWI data

Tensor reconstruction with GE DWI data
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10:52 am
March 11, 2010


cibuthomas

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Hello

I have DWI data in 60 direction that were collected in 4 runs. DTK recognizes the data as 4 unique series. Is there anyway I can use DTK to combine the data into a single series so that DTK can do the reconstruction?

Thank you

Cibu

1:58 pm
March 11, 2010


Ruopeng

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Post edited 1:59 pm – March 11, 2010 by Ruopeng

Hi Cibu,

In that case, you will have to convert the images into individual 3D volumes and name them with numbered suffix, such xxx001.nii, xxx002.nii… xxx060.nii… DTK can take a series of 3D volume files.

Ruopeng

4:33 pm
March 12, 2010


cibuthomas

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Thanks Roupeng

Trouble is the b = 0 volumes are scattered across the 4 runs. Anyway, I used TORTOISE to get a single analyze volume with the b = 0 volume (N=10) first followed by b = 300 (N = 10) and b max = 1100 (N = 60 directions). I have the raw data set in FSL format, so I have the bvecs and bval files in seperate files. My question is how can I make a gradient table using the bvals and bvecs so that DTK understands the raw data.

 

cheers

Cibu

10:57 pm
March 14, 2010


Ruopeng

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The current version of DTK can not process data set with multiple high b values. Also, it requires all the b0 volumes at the top of the series. But the upcoming release (coming very soon!) is going to support multiple high b values as well as b0 volumes at anywhere in the series.

Ruopeng

5:03 pm
March 16, 2010


Ruopeng

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You might have noticed that a new version of Diffusion Toolkit has been released. This version will allow you to put b0 vector in the gradient table. You can also specify b value as the 4th component in the table. You still however need to number your image files correctly in this case because they are not from one series.

Ruopeng
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