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open-discussion > Problem with "IBSR_V2.0_nifti_stripped" NIfTI files
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Jul 17, 2020 08:07 AM | Vikas V
Problem with "IBSR_V2.0_nifti_stripped" NIfTI files
I have a question regarding the data present
in"IBSR_V2.0_nifti_stripped", e.g, IBSR_01_ana.zip.
I see few issues with the pixel data, when I checked the pixel spacing, this looks more like a non-square pixel data, is that right?
If I load the data in a nifti viewer or convert it to DICOM and load it in a DICOM viewer I can clear see the data is stretched which indicates the spacings are incorrect.
For example:
IBSR_01_ana.nii has has non-square pixels and spacing of [0.9375, 1.5, 0.9375].
This should most likely become [0.9375, 0.9375, 1.5] which matches expectations that in-plane scan resolution (XY) is higher than in the acquisition direction (slice distance).
Is this Nifti generated correctly or how was this data acquired?
I see few issues with the pixel data, when I checked the pixel spacing, this looks more like a non-square pixel data, is that right?
If I load the data in a nifti viewer or convert it to DICOM and load it in a DICOM viewer I can clear see the data is stretched which indicates the spacings are incorrect.
For example:
IBSR_01_ana.nii has has non-square pixels and spacing of [0.9375, 1.5, 0.9375].
This should most likely become [0.9375, 0.9375, 1.5] which matches expectations that in-plane scan resolution (XY) is higher than in the acquisition direction (slice distance).
Is this Nifti generated correctly or how was this data acquired?
Jul 17, 2020 01:07 PM | Andrew Worth
RE: Problem with "IBSR_V2.0_nifti_stripped" NIfTI files
Hello Vicas V,
The attached screenshots show how that file looks using itk-snap. You are correct: the resolution is not isotropic.
Andy.
Originally posted by Vikas V:
The attached screenshots show how that file looks using itk-snap. You are correct: the resolution is not isotropic.
Andy.
Originally posted by Vikas V:
I have a question regarding the data
present in"IBSR_V2.0_nifti_stripped", e.g, IBSR_01_ana.zip.
I see few issues with the pixel data, when I checked the pixel spacing, this looks more like a non-square pixel data, is that right?
If I load the data in a nifti viewer or convert it to DICOM and load it in a DICOM viewer I can clear see the data is stretched which indicates the spacings are incorrect.
For example:
IBSR_01_ana.nii has has non-square pixels and spacing of [0.9375, 1.5, 0.9375].
This should most likely become [0.9375, 0.9375, 1.5] which matches expectations that in-plane scan resolution (XY) is higher than in the acquisition direction (slice distance).
Is this Nifti generated correctly or how was this data acquired?
I see few issues with the pixel data, when I checked the pixel spacing, this looks more like a non-square pixel data, is that right?
If I load the data in a nifti viewer or convert it to DICOM and load it in a DICOM viewer I can clear see the data is stretched which indicates the spacings are incorrect.
For example:
IBSR_01_ana.nii has has non-square pixels and spacing of [0.9375, 1.5, 0.9375].
This should most likely become [0.9375, 0.9375, 1.5] which matches expectations that in-plane scan resolution (XY) is higher than in the acquisition direction (slice distance).
Is this Nifti generated correctly or how was this data acquired?
Jul 17, 2020 01:07 PM | Andrew Worth
RE: Problem with "IBSR_V2.0_nifti_stripped" NIfTI files
Hmmm, only one screen shot made it the first time. Here is
the other (attached).
Andy.
Andy.