Comments (3)
This type of layered image info is expected in 3D backscatter imaging.
from mricrogl.
MRIcroGL is able to use the S-Form and Q-Form to orient the closest orthogonal orientation and scale. However, it retains rectangular voxels. So with respect to the affine if handles the rotation, translation and scale but ignores the shear.
You may want to look at NiiVue or FSLeyes, both of which can show voxels in either image space or world space. You need to be aware that the NIfTI format has two spatial representations: the Q-Form (quaternion) stores 9 degrees of freedom (translation, rotation, scale each in 3 dimensions) while the S-Form (matrix) stores 12 DoF (adding shear). Therefore, to preserve shear you must properly define the S-Form of your NIfTI header.
Since most tools (including those built using the popular VTK library) assume that volumes do not have shear, another alternative is to resample your data into a large volume. If your source data is in DICOM format, dcm2niix can do this for you. For sample DICOM and dcm2niix converted data, see dcm_qa_ct where the DICOM images have gantry tilt, and dcm2nixi creates two volumes: one where the shear is reported in the S-Form, the other (_tilt
) where the data is resampled.
from mricrogl.
@neurolabusc Thanks for pointing out, it seems NiiVue is pretty fit for my use! My files are not from prebuilt commercial systems that comes with DICOM format, but instead we are developing new systems and thus chose Nifti as a simple format for storing scintilator or semiconductor detector event count. DICOM is simply an overkill for prototypes.
from mricrogl.
Related Issues (20)
- Incompatibility of v1.2.20220720 with Ubuntu 18.04 circumstance HOT 4
- Borg_Error for large t (4th dimension) nii.gz files in Windows HOT 2
- Saving T1 + spmT overlay as a single combined nifti file HOT 5
- MRIcroGL overlay render depth HOT 2
- Opening .nii files with MRIcroGL does not work: failed to load function PyLong_FromUnicode
- How to add packages to python for scripting HOT 1
- Loads blank window on startup, is this the “long wait” from the notification? HOT 4
- cannot install the linux version on WSL (Ubuntu) HOT 6
- Decrease line thickness in glass brain? HOT 1
- Is a MNI152 to SPM152 transformation available? HOT 1
- MRICroGL software query HOT 1
- MRIcroGL query HOT 1
- Creating random color look up table HOT 1
- Looking for script command for "Hide voxels with zero intensity" HOT 2
- Retain thresholds when moving across volumes of 4D NIfTI HOT 3
- [BUG] MRIcroGL shows wrong path when hovering over overlays. HOT 3
- Module not found error with scripting HOT 6
- MNI template version
- py script function bmptransparent does not work
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from mricrogl.