dcm2niix
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| dcm2niix | GDCM | |
|---|---|---|
| 6 | - | |
| 807 | 336 | |
| 4.7% | - | |
| 7.6 | 8.5 | |
| 6 days ago | 5 days ago | |
| C++ | C++ | |
| GNU General Public License v3.0 or later | GNU General Public License v3.0 or later |
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dcm2niix
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I have a doubt in brain MRI scan
Keep in mind that DICOM images are always converted to the NIfTI format when dealing with neuroimaging data, so the different software are expecting this image type. You should always keep the original DICOM files in your archive, but convert them to NIfTI and use that as your raw data input. To convert DICOM to NIfTI, you can use a tool like dcm2niix dcm2niix.
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Conversion of DICOM to .nii.gz
When I try to execute the .exe in the link you have provided the program does not run. However, according to this site: https://github.com/rordenlab/dcm2niix! the niix is included in MRIcroGL which I have tried.
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Can somebody help me quantify spatial resolution in CT scans of mice?
The spatial resolution of the scan is typically in the DICOM header, isn't it? Maybe try running the DICOM through something like dcm2niix (https://github.com/rordenlab/dcm2niix) which will convert to a NIFTI formatted image and generate a JSON file from the header. The header support isn't complete, so it might not get things correct from your CT image (or from an animal scanner for that matter), but it's worth a shot. I imagine there are similar tools for CT.
- Full-size 3D print of my brain
- Convert DICOM Slices to Nifti Using Nibabel(Python)
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Tracking mentions began in Dec 2020.
What are some alternatives?
jpeg-autorotate - 📸 Node module to rotate JPEG images based on EXIF orientation.
OpenCV - Open Source Computer Vision Library
brainflow - BrainFlow is a library intended to obtain, parse and analyze EEG, EMG, ECG and other kinds of data from biosensors
ITK - Insight Toolkit (ITK) -- Official Repository. ITK builds on a proven, spatially-oriented architecture for processing, segmentation, and registration of scientific images in two, three, or more dimensions.
gdl - GDL - GNU Data Language
Video++ - Video++, a C++14 high performance video and image processing library.
MRIcroGL - v1.2 GLSL volume rendering. Able to view NIfTI, DICOM, MGH, MHD, NRRD, AFNI format images.
VTK - Mirror of Visualization Toolkit repository
DicomToMesh - A command line tool to transform a DICOM volume into a 3d surface mesh (obj, stl or ply). Several mesh processing routines can be enabled, such as mesh reduction, smoothing or cleaning. Works on Linux, OSX and Windows.
OpenMVG (open Multiple View Geometry) - open Multiple View Geometry library. Basis for 3D computer vision and Structure from Motion.
simnibs - Simulation of Non-Invasive Brain Stimulation
OpenImageIO - Reading, writing, and processing images in a wide variety of file formats, using a format-agnostic API, aimed at VFX applications.