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questions > RE: Question about bvec (diffusion MR) converted using dcm2niix
Sep 19, 2019 06:09 PM | eegee
RE: Question about bvec (diffusion MR) converted using dcm2niix
For the first part of the question, I think the answer is yes.
If you refer to the illustration, P R S corresponds to (ant-pos, left-right, up-down) in my protocol.
Thus vector[0] =( 0.0804, -0.3699, 0.9256) ... was actually giving the scanner the values in "ant-pos, left-right, up-down" direction.
This case, the actual gradient will be y = 0.0804, x = -0.3699, z = 0.9256 in terms of scanner, and dcm2nii is actually giving these numbers in x y z directions.
It will be good if dcm2niix can read coordinate system information from DICOM file and indicate whether the gradient was in PRS or XYZ. However, .json file does not provide this detail to begin with, and I assume Siemens is not outputting that information. I assume it's a Siemens issue then.
What I will do, is I will try collecting Diffusion data using both PRS and XYZ coordinate system and see what dcm2nii creates. If there's still an issue I will reply to this again and post it to github.
For the second part of the question, yes, you are definitely correct. This is just an illustration in our case. XYZ as well as PRS can be different depending on setups of the scanner/readout directions.
Thank you again,
If you refer to the illustration, P R S corresponds to (ant-pos, left-right, up-down) in my protocol.
Thus vector[0] =( 0.0804, -0.3699, 0.9256) ... was actually giving the scanner the values in "ant-pos, left-right, up-down" direction.
This case, the actual gradient will be y = 0.0804, x = -0.3699, z = 0.9256 in terms of scanner, and dcm2nii is actually giving these numbers in x y z directions.
It will be good if dcm2niix can read coordinate system information from DICOM file and indicate whether the gradient was in PRS or XYZ. However, .json file does not provide this detail to begin with, and I assume Siemens is not outputting that information. I assume it's a Siemens issue then.
What I will do, is I will try collecting Diffusion data using both PRS and XYZ coordinate system and see what dcm2nii creates. If there's still an issue I will reply to this again and post it to github.
For the second part of the question, yes, you are definitely correct. This is just an illustration in our case. XYZ as well as PRS can be different depending on setups of the scanner/readout directions.
Thank you again,
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Title | Author | Date |
---|---|---|
eegee | Sep 19, 2019 | |
Chris Rorden | Sep 19, 2019 | |
eegee | Sep 19, 2019 | |
eegee | Sep 20, 2019 | |
Chris Rorden | Sep 20, 2019 | |
Chris Rorden | Sep 19, 2019 | |
eegee | Sep 19, 2019 | |