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rordenlab / dcm2niix

dcm2nii DICOM to NIfTI converter: compiled versions available from NITRC
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Different study/data time, -m option not working #846

Closed javijv4 closed 3 months ago

javijv4 commented 3 months ago

Describe the bug

I am using dcm2niix to convert a long axis cardiac MRI image. It contains 4D data, with the images containing only one slice but 24 frames. When I try using dcm2niix I get two .nii files instead of one.

To reproduce

Steps to reproduce the behavior:

  1. Run the command 'dcm2niix -m -y 1401_sBTFE_BH_3CH'
  2. Two nifti files are created, one with 23 frames and the other with 1.

Expected behavior

I believe the dcm2niix is splitting the data because of the study time. I tried using the -m -y option but the behavior was the same.

Output log

''' Chris Rorden's dcm2niiX version v1.0.20240202 (JP2:OpenJPEG) (JP-LS:CharLS) GCC8.4.0 x86-64 (64-bit Linux) Found 24 DICOM file(s) Slices not stacked: Study Date/Time (0008,0020;0008,0030) varies 20240704183635.000000000000 ~= 20240704183636.000000000000 Warning: All images appear to be a single slice - please check slice/vector orientation ::autoBids:Philips pulseSeq:'B-TFE' scanSeq:'GR' seqVariant:'SK' Philips Scaling Values RS:RI:SS = 2.21441:0:0.0929865 (see PMC3998685) Convert 23 DICOM as /home/jilberto/Dropbox (University of Michigan)/Projects/Modeling/nnUNetv2/Ot-LA/data/DoP1/tmp/1401_sBTFE_BH_3CH/1401_sBTFE_BH_3CH_sBTFE_BH_3CH_20240704183635_1401b (320x320x1x23) ::autoBids:Philips pulseSeq:'B-TFE' scanSeq:'GR' seqVariant:'SK' Philips Scaling Values RS:RI:SS = 2.21441:0:0.0929865 (see PMC3998685) Convert 1 DICOM as /home/jilberto/Dropbox (University of Michigan)/Projects/Modeling/nnUNetv2/Ot-LA/data/DoP1/tmp/1401_sBTFE_BH_3CH/1401_sBTFE_BH_3CH_sBTFE_BH_3CH_20240704183636_1401b (320x320x1x1) Conversion required 0.015904 seconds (0.015891 for core code). '''

Version

neurolabusc commented 3 months ago

dcm2niix assumes that DICOM images are truthful. It appears that the study time appears to exhibit a rounding error. I suggest you contact the Philips Clinical Scientist associated with this scanner to resolve the issue. For data acquired, you might want to see if you can use dcmodify to make these values consistent for your dataset.