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TOPIC: DTI data format

DTI data format 5 years 8 months ago #288

  • ChrRossmanith
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Hi,

after starting to use medinria with the provided sample data I'd like to import our own data.

Acquisition: 3 repetitions with 1 b0 volume and 30 b1000 volumes each ( = 3 * (1+30) volumes )

As far as I understand the gradient vector file format there is no line for the b0 volume. Am I supposed to provide only one b0 volume as the first volume in the 4D input data, i.e. select one of the three available volumes or the calculate the average? Are repeated gradient vector lines for the b1000 volumes allowed?

Thank you for any hints,
Christina Rossmanith
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DTI data format 5 years 8 months ago #290

  • ocommowick
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Hi,

You have two ways to provide gradients to medinria. The first one is to use a txt file in the same way as provided with the example data (gradient7.txt). In that case, the first B0 line (corresponding to the first volume of the 4d data) has to be omitted, but all other gradients (including 0 0 0 lines for B0) have to be provided. The other way is to provide a bvec file which is often an output of external dicom converters such as dcm2nii.

In any case, gradients can be several times the same, the algorithm won't mind and will use all provided values to estimate the tensors.

Hope that helps
Olivier
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DTI data format 5 years 8 months ago #296

  • ChrRossmanith
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Hi,

that helped indeed. And rises new questions :-)

When importing a 4D nifti volume and the corresponding gradient vector file the patient name is lost. I've found out that I can create a new patient in the data base manually. Is there a way to assign a 4D nifti volume to a patient? Currently all imported data is belonging to John Doe...

What about eddy current correction: Use e.g. fsl's eddy_correct and then proceed with medinria?

Christina
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DTI data format 5 years 7 months ago #304

  • ocommowick
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Hi,

I'm answering quite a bit late. Yes, you can move an image from one patient to another. For that, you have to go in the browser area, in the local database of medinria. There, you can create an empty patient and empty study. These can then be renamed just by clicking on it and typing a new name. Once your new patient and study are created, you can drag and drop the image you want to move to its new destination.

As for eddy current correction, it is not in medinria yet, but you can do any processing you want outside of medinria. As long as your data is in a regular ITK file format, medinria will be able to read it.

Olivier
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