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questions > GE diffusion data FFS and in spatially descending order
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Apr 19, 2023 01:04 PM | Manuela Zimmer
GE diffusion data FFS and in spatially descending order
Hi everyone,
I have diffusion MRI data from a GE Signa Premier that was acquired FFS (feet first supine) and in spatially descending order (head-to-foot) with Phase Encoding direction (0018,1312) "COL".
It is a scan of the lower leg which I want to use for skeletal muscle modelling purposes.
When using dcm2niix (v1.0.20220720), I obtain the following two messages/warnings:
Here (https://www.na-mic.org/wiki/NAMIC_Wiki:D...), I found the following hint:
"The gradient directions are in the image (rather than scanner bore) frame of reference. The interpretation depends on the Phase Encoding direction (0018,1312). If 0018,1312 is "COL" than 0019,10bb refers to the image columns (i), 0019,10bc refers to the image rows (j) and 0019,10bd refers to the slices (k). If 0018,1312 is "ROW" [...].
There are two caveats: This assumes that your slices are stacked in spatially ascending order (head to foot for axial acquisitions) regardless of the order that they were saved to disk (which appears to vary depending on how the user plans the scan). You need to adjust the polarity of these directions to match the expectations of the software used for fitting."
How do I need to adjust the polarity of the gradient directions?
Do I need to modify the DICOM images before converting to nifti because they are FFS instead of HFS?
There is no error for dm2nixx. Therefore, the nifti file, bvec and bval files are generated.
The nifti file looks correct (viewing the 4D matrix with fsleyes) and the matrix size is as expected (256x256x60x32).
However, when calculating the eigenvectors (and later performing the tractography), we can observe anatomical unexpected (incorrect) directions.
Any help is appreciated. Thanks!
I have diffusion MRI data from a GE Signa Premier that was acquired FFS (feet first supine) and in spatially descending order (head-to-foot) with Phase Encoding direction (0018,1312) "COL".
It is a scan of the lower leg which I want to use for skeletal muscle modelling purposes.
When using dcm2niix (v1.0.20220720), I obtain the following two messages/warnings:
- Warning: Unable to compute slice times for GE Diffusion
- GE DTI directions require head first supine acquisition
Here (https://www.na-mic.org/wiki/NAMIC_Wiki:D...), I found the following hint:
"The gradient directions are in the image (rather than scanner bore) frame of reference. The interpretation depends on the Phase Encoding direction (0018,1312). If 0018,1312 is "COL" than 0019,10bb refers to the image columns (i), 0019,10bc refers to the image rows (j) and 0019,10bd refers to the slices (k). If 0018,1312 is "ROW" [...].
There are two caveats: This assumes that your slices are stacked in spatially ascending order (head to foot for axial acquisitions) regardless of the order that they were saved to disk (which appears to vary depending on how the user plans the scan). You need to adjust the polarity of these directions to match the expectations of the software used for fitting."
How do I need to adjust the polarity of the gradient directions?
Do I need to modify the DICOM images before converting to nifti because they are FFS instead of HFS?
There is no error for dm2nixx. Therefore, the nifti file, bvec and bval files are generated.
The nifti file looks correct (viewing the 4D matrix with fsleyes) and the matrix size is as expected (256x256x60x32).
However, when calculating the eigenvectors (and later performing the tractography), we can observe anatomical unexpected (incorrect) directions.
Any help is appreciated. Thanks!
Apr 19, 2023 02:04 PM | Chris Rorden
RE: GE diffusion data FFS and in spatially descending order
We do not have GE hardware at my site. FFS generates an error as it
has never been validated. You could try reversing the polarity of
the 3rd component of the bvec file to see if that resolves your
issue. You will want to carefully validate using the method
described here
https://www.nitrc.org/docman/?group_id=880
https://www.nitrc.org/docman/?group_id=880