help
help > RE: VOI in mm cube?
May 29, 2022 07:05 PM | tammartru
RE: VOI in mm cube?
Dear MriCron expert!
Flowing the suggested script for calculating images volume (https://github.com/rordenlab/spmScripts/...)
I am not sure it is the right script, because it seems to only calculate number of Nan voxels.
Could you please direct me to the script calculating ROIs volumes?
Thank you very much!
Tammar
Originally posted by Chris Rorden:
Flowing the suggested script for calculating images volume (https://github.com/rordenlab/spmScripts/...)
I am not sure it is the right script, because it seems to only calculate number of Nan voxels.
Could you please direct me to the script calculating ROIs volumes?
Thank you very much!
Tammar
Originally posted by Chris Rorden:
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.
Threaded View
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 | |