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help > RE: VOI in mm cube?
Apr 9, 2021 12:04 PM | Chris Rorden
RE: VOI in mm cube?
The distance between voxels centers in the row, column and slice
directions is stored as pixdim[1], pixdim[2], pixdim[3]
in the NIfTI header. Just make sure the image specifies
NIFTI_UNITS_MM
https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h
I am surprised that you list negative values, as usually these are absolute values. Not sure which tool described these. You can also determine the voxel size from the s-form or q-form, where negative values would create a negative determinant (e.g. an image that is mirrored with respect to canonical space).
Your formula looks fine, though I would use absolute values for volume.
If you have a lot of images, you would be better off writing a Matlab or Python script. MRIcroGL can save images as either .nii, .nii.gz or .voi format - in reality the .voi format is just a .nii.gz (with the extension telling the software to treat it as a discrete rather than continuous image). A script like this one
https://github.com/rordenlab/spmScripts/...
could easily be modified to report volumes for hundreds of images with whatever precision you prefer.
https://nifti.nimh.nih.gov/pub/dist/src/niftilib/nifti1.h
I am surprised that you list negative values, as usually these are absolute values. Not sure which tool described these. You can also determine the voxel size from the s-form or q-form, where negative values would create a negative determinant (e.g. an image that is mirrored with respect to canonical space).
Your formula looks fine, though I would use absolute values for volume.
If you have a lot of images, you would be better off writing a Matlab or Python script. MRIcroGL can save images as either .nii, .nii.gz or .voi format - in reality the .voi format is just a .nii.gz (with the extension telling the software to treat it as a discrete rather than continuous image). A script like this one
https://github.com/rordenlab/spmScripts/...
could easily be modified to report volumes for hundreds of images with whatever precision you prefer.
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Title | Author | Date |
---|---|---|
alexpcg10 | Apr 8, 2021 | |
alexpcg10 | Apr 11, 2021 | |
Chris Rorden | Apr 11, 2021 | |
Chris Rorden | Apr 8, 2021 | |
alexpcg10 | Apr 9, 2021 | |
Chris Rorden | Apr 9, 2021 | |
tammartru | May 29, 2022 | |
Chris Rorden | May 30, 2022 | |
tammartru | May 31, 2022 | |