Comments (2)
I believe this is a duplicate of
http://www.nitrc.org/tracker/?func=detail&atid=3335&aid=8118&group_id=880
I think you tried to convert a derived image. In particular the file name "COLFA" probably refers to a derived "COLOR FRACTIONAL ANISOTROPY" image
I think you should update to version 28June2016. If I am correct it will change the warning to the less shrill and more specific:
Unable to determine spatial orientation: 0020,0037 missing (probably not a problem: derived image)
Explanation: I think this is a derived image (FA/ADC maps based on series of DWI scans) rather than a raw image. Be warned that Siemens does not preserve spatial coordinates when computing derived images. This is usually not an issue for scientists: the derived maps are stored with very poor precision (8-bit RGB) and most imaging software (FSL/SPM/AFNI) will not process RGB images. Furthermore, you can derive much nicer FA/ADC maps after you undistorted the raw images with Eddy/Topup. Personally, on our Prisma I open the protocol with the ExamExplorer, go to the "Diff" tab and uncheck the "ADC maps" and "FA maps" check boxes so the console does not generate derived images.
Despite my clarified note to the user, I do still think this is a serious error. I do suggest you follow my lead and encourage Siemens to preserve the spatial encoding when generating derived images. No DICOM viewer will be able to determine spatial orientation without this. For example, if you drop one of these images on a tool popular with clinicians such as Osirix, they are not shown any labels for spatial orientation, so the user will have to know which is the left and right side of the brain.
from dcm2niix.
THANK YOU for the detailed explanation
from dcm2niix.
Related Issues (20)
- Estimated Gantry Tilt -nan(ind), but Gantry Tilt field is 0 HOT 5
- Please provide instructions HOT 1
- Unable to find any DICOM images if the absolute path of input folder too long HOT 3
- Extract kVp into the json file from DICOM header HOT 1
- Series split into multiple NIfTI volumes unexpectedly HOT 7
- setBidsGE fails to recognize Gradient Echo EPI HOT 4
- Slice timing missing in the json file HOT 2
- Q about where json gets written HOT 6
- Filename oddity in 20240202 for Philips DWI HOT 10
- GE UHP/7T Diffusion SliceTiming HOT 5
- Possible incorrect SliceTiming HOT 16
- Siemens conversion problems (Magnetom Altea) HOT 2
- error dcm2niix using dcm2bids HOT 1
- PET json information HOT 12
- Inquiry on DICOM to NIfTi HOT 4
- Siemens 2D epi TR is incorrect HOT 2
- dcm2niix is incorrectly attempting to use a JPEG:Lossless transfer syntax that was set inside an Original Attributes Sequence HOT 1
- GE AcquisitionDuration HOT 6
- Incorrect Slice/Vol Order After Site Updated Philips Software (Ingenia version 11.1) HOT 11
- Return status bug (incorrectly reported error) v1.0.20240202 HOT 12
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 dcm2niix.