dcm2niix does not recognize DICOMs #157
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Can you build the latest version and test that it works with all of your image samples. The image that you had problems with was very odd - it reports a Icon Image Sequence (0088,0200) with specific attributes (e.g. palette rather than scalar colors) but does not actually include the icon image. My software includes some kludges to deal with a bug in how GE's PACS system would insert icons that violated the DICOM standard. I assume someone manipulated these images to remove the icons, but did not remove the icon attributes. The current version of my software should generate warnings when it detects this odd behavior, but it should convert the images correctly. |
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I've tested it and everything seems to be fine now. Thank you! |
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@neurolabusc I'm also using ppmi (subject id: 3320) and having the same problem while converting with dcm2niix. Was using the version v1.0.20170724 and updated to version v1.0.20121215 and the problem persists. Any solution would be helpful. Thanks |
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This is another example of the same defective images. You have three choices:
You may also want to contact the PPMI and ask them to clean up their DICOMs, as these images may cause problems with other/future tools. |
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I went with option 3 and it solved the problem for this particular image. |
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Hi, I am having problems reading and converting Dicom images generates from a new Siemens Trio scanner. The dicom image is found in the folder but not recognised as valid by the latest version of dcm2niix. The file header contains meta-data (see info below). The dicom files also contain physiological data - perhaps that is the problem? Thank you -- Filename: '/Volumes/fm_data/FAPIA/data/raw/26652_0014_00001.dcm' |
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dcm2niix is designed to convert DICOM images to the NIfTI image format. It does not convert non-image based data such as physiological and audio files, as the NIfTI specification does not describe how to encode these. In your example, note that this is not an image, as revealed by the |
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It looks like this might be an example of the physio log DICOMs output by the newer CMRR multiband sequences. Feel free to use/adapt the dcm2physio.py script from https://github.com/adolphslab/mriphysio to extract the physiological waveforms from these files. |
* commit 'v1.0.20171215-29-ga662295': Update GE and PAR/REC notes. Add warnings for novel PARREC data, use GE proprietary sliceorder Restore support for PAR/REC dwi with included ADC/Isotropic Use ImageType (0008,0008) to split phase and magnitude (rordenlab#170) Improved GE support Further PARREC tuning Improved Philips PARREC support Better PAR/REC error reporting 0020,9157 does not necessarily index gradient directions from 1..n (e.g. 2...37 for ADNI 018_S_4868) Preliminary attempt to support PAR/REC with arbitrary slice orders (e.g. order reconstructed, not acquired) Restore support for compressed DICOM (Jon Clayden) Restore ability to handle DICOMs files with Icon Image Fixes for Philips rordenlab#165 rordenlab#170 ENH: minor - consistent formatting (%?=description) of template keywords for -f More Philips enhanced support Partial solution for rordenlab#165 Experimental SQ skipping: Philips private use of public tags rordenlab#165 Fix for rordenlab#168 Remove GCC version >= 7.1.0 warning: snprintf output between 1 and 256 bytes into a destination of size 24 Fix for rordenlab#157
I am having problems converting several DICOM files from the PPMI database. dcm2niix claims that there are no dicom files in the folder:
However, dcm2nii is very happy to do the conversion:
The converted images look normal.
One example subject from the PPMI database is ID = 3587.
Any ideas what might be causing this? Thanks!
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