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False detection of duplicate slices #168
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Jon |
I've scrubbed the DICOMs to the point that I can send you a dataset that shows the problem - what's the best way to get the data over to you? I tried building from source and the problem is still present. I'm not involved in acquiring the data so we're stuck working with what the scanning sites for the study provide otherwise I would try bypassing the PACS. |
Why not put them all in a zip archive and send a link to my email (lastname@sc.edu) |
@jstutters please test the latest master source code, and close this issue if it works for your data. In your example the standard item "ImageNumber" (0020,0013) is used correctly in the main header and again with a different/contradictory value in the private SQ 2001,9000. This behavior seems to be technically legal (ftp://medical.nema.org/medical/dicom/final/cp758_ft.pdf). This issue is a specific form of the general issue described in 165. |
Thanks! That seems to have solved the problem. Apologies if this was fixed earlier, I may have been a bit confused about which of rordenlab/dcm2niix and neurolabusc/dcm2niix had the most recent changes. |
* 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'm having a problem with the conversion of some DICOMs from a Philips Achieva. dicm2niix is falsely detecting duplicate slices in some 2D sequences. I've checked the ImagePositionPatient header and it varies by 3mm per slice in the Z direction as expected so I'm happy that there aren't any duplicate slices. The Matlab dicm2nii script is able to convert the sequence correctly to a 46 slice NIFTI. The same issue is found in dcm2niix v1.0.20170623, the latest stable release and the git master. I'm not able to provide the DICOM data unfortunately but I can update this report with more information from the headers if that would be helpful.
Program output:
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