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questions > RE: dcm2niix Siemens Mosaic
Feb 26, 2018 11:02 AM | Chris Rorden
RE: dcm2niix Siemens Mosaic
Jessica,
I really can not understand the issue you are having from your description. The dcm2niix software should create one 3D volume for every 2D multi-slice mosaic. For fMRI and DWI inputs, it should create a 4D output, where every volume describes a different timepoint (fMRI) or direction (DWI).
The warnings are typical. For most Siemens systems we want to combine acquisitions into a single 4D dataset, your images do not appear to report slice timing (perhaps these images are saved without a CSA header that provides this information) and while the directions for DWI are pretty well known for Siemens, it is a good idea to check the conversion of these directions from scanner space to image space as described in the 'dedicated document' you can download from here
https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Diffusion_Tensor_Imaging
My advice is to make sure that you are using the latest version of dcm2niix (v1.0.20171215)
https://github.com/rordenlab/dcm2niix/releases
Aso, due to the CSA warning it might make sense to see if you can get the images directly from the scanner, as it is possible that a PACS anonymization routine is stripping off the CSA details that we use to compute some sequence information. If this does not resolve the issue, please submit a new "issue" on the dcm2niix github web page.
I really can not understand the issue you are having from your description. The dcm2niix software should create one 3D volume for every 2D multi-slice mosaic. For fMRI and DWI inputs, it should create a 4D output, where every volume describes a different timepoint (fMRI) or direction (DWI).
The warnings are typical. For most Siemens systems we want to combine acquisitions into a single 4D dataset, your images do not appear to report slice timing (perhaps these images are saved without a CSA header that provides this information) and while the directions for DWI are pretty well known for Siemens, it is a good idea to check the conversion of these directions from scanner space to image space as described in the 'dedicated document' you can download from here
https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Diffusion_Tensor_Imaging
My advice is to make sure that you are using the latest version of dcm2niix (v1.0.20171215)
https://github.com/rordenlab/dcm2niix/releases
Aso, due to the CSA warning it might make sense to see if you can get the images directly from the scanner, as it is possible that a PACS anonymization routine is stripping off the CSA details that we use to compute some sequence information. If this does not resolve the issue, please submit a new "issue" on the dcm2niix github web page.
Threaded View
Title | Author | Date |
---|---|---|
Jessica Lee | Feb 26, 2018 | |
Chris Rorden | Feb 26, 2018 | |