osirix
dcm2niix
osirix | dcm2niix | |
---|---|---|
5 | 6 | |
348 | 816 | |
0.3% | 1.1% | |
2.6 | 7.4 | |
5 months ago | 13 days ago | |
C++ | C++ | |
- | GNU General Public License v3.0 or later |
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osirix
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I present to you the Bramp - a Hue powered lamp made of a 3D print of my own brain
OsirisX for reading and manipulating the DICOM images
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CT scan of a patient who had swallowed 63 packets of cocaine. The packets were successfully evacuated using laxatives.
This looks like a 3D reconstruction of a CT image, so it can be colored however the authors want it to be colored. CT imaging in and of itself involves shooting x-rays at the subject being imaged and (essentially) measuring what comes out the other side. As such, CT results (as far as I know) don't have colors 'baked into them'; the information in each pixel is an intensity value that ranges from 0 (no x-rays made it through) to 1 (the detector is saturated with x-rays; 255 may be more realistic than 1 here because 255 is the max number that can be stored in an 8-bit byte). So basically what I think the authors did here is acquire the CT image and then use a medical image viewer like OsiriX to generate a 3D reconstruction of that image. Once such a reconstruction is made, changing colors in it is as simple as changing colors in any other 3D editing software. So in my opinion, the novel/interesting thing here is the thing being imaged, not the image itself (although I will say it's interesting that they were able to isolate JUST the cocaine packets and the bone, with all other soft tissue and organs removed)
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Can someone please look at my MRI and tell me what's going on!
You can view the images with https://www.osirix-viewer.com but I would take that disc and see a number of physicians (orthopedic, neuro, physiatry) and ask them for their opinion and to please explain what they see. They should pull the images up and evaluate the spine axially and sagittally (top-down, left-to-right), level by level and point out features to you: discs, exiting nerve roots, etc. It'll become pretty obvious if there's a pattern: stenosis, arthritis, overgrown ligament, etc... Also ask them what they think is appropriate for treatment.
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Reading MRI CD help
I used https://www.osirix-viewer.com/ and could see the MRI easily. I used this CD reader https://www.amazon.com/gp/product/B07PV958PN/ref=ppx_yo_dt_b_asin_title_o00_s00?ie=UTF8&psc=1
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Ask HN: What is the most interesting FOSS that most people don't know about?
OsiriX viewer. I got it to view my before/after CT scans to see exactly what happened in surgery. It's pretty wild being able to see inside yourself.
The site: https://www.osirix-viewer.com
The repo: https://github.com/pixmeo/osirix
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)
What are some alternatives?
reactos - A free Windows-compatible Operating System
jpeg-autorotate - 📸 Node module to rotate JPEG images based on EXIF orientation.
brainflow - BrainFlow is a library intended to obtain, parse and analyze EEG, EMG, ECG and other kinds of data from biosensors
gdl - GDL - GNU Data Language
MRIcroGL - v1.2 GLSL volume rendering. Able to view NIfTI, DICOM, MGH, MHD, NRRD, AFNI format images.
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.
ESP32-targz - 🗜️ An Arduino library to unpack/uncompress tar, gz, and tar.gz files on ESP32 and ESP8266
simnibs - Simulation of Non-Invasive Brain Stimulation
3dprintyourbrain - How to 3D print your brain from a T1 MRI image.
gonii - Standalone NIfTI file parser
GDCM - Grassroots DICOM read-only mirror. Only for Pull Request. Please report bug at http://sf.net/p/gdcm