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questions > RE: dcm2nii DTI Data
Feb 3, 2017 03:02 PM | Chris Rorden
RE: dcm2nii DTI Data
Graham-
It would help if you could provide a bit more information, e.g. "I am running dcm2nii 2May2016 on a Windows to convert data from our Siemens Trio with B19". However, I have a few thoughts:
1.) Have you tried dcm2niix (which comes with MRIcroGL) instead of dcm2nii (which comes with MRIcron)? While I hope my old software is mature and stable, vendors re-interpret the DICOM standard and therefore having modern software helps.
2.) The location of the DTI tags varies by vendor, for Siemens I peak inside the proprietary CSA header.
https://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI
3.) My software only generates bvec/bval files when there is variability in the B-values. If you acquire a sequence with all B=0 values, no text file is created (as from a software point of view this looks like a fMRI sequence). If you acquire B=0 images in a separate session and combine them with b-weighted images for analyses you need to create bvec and bval files for your B=0 series (e.g. https://github.com/rordenlab/spmScripts/...). Most DTI sequences have at least one B=0 image as well as the B-weighted images, so it should detect normal DTI scans fine. I would recommend setting up your DTI sequence to have a few B=0 images embedded with the weighted images, as this will improve measures like MD and DK (for my hints on DTI see here http://www.mccauslandcenter.sc.edu/crnl/...).
I tested my software on sequences from all vendors
https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Diffusion_Tensor_Imaging
But it is possible that your vendor has introduced its own private tags or methods to encode diffusion data. If so you can either provide sample images or create an updated version of dcm2niix that fixes the problem and submit a pull request on Github.
-c
It would help if you could provide a bit more information, e.g. "I am running dcm2nii 2May2016 on a Windows to convert data from our Siemens Trio with B19". However, I have a few thoughts:
1.) Have you tried dcm2niix (which comes with MRIcroGL) instead of dcm2nii (which comes with MRIcron)? While I hope my old software is mature and stable, vendors re-interpret the DICOM standard and therefore having modern software helps.
2.) The location of the DTI tags varies by vendor, for Siemens I peak inside the proprietary CSA header.
https://www.na-mic.org/Wiki/index.php/NAMIC_Wiki:DTI:DICOM_for_DWI_and_DTI
3.) My software only generates bvec/bval files when there is variability in the B-values. If you acquire a sequence with all B=0 values, no text file is created (as from a software point of view this looks like a fMRI sequence). If you acquire B=0 images in a separate session and combine them with b-weighted images for analyses you need to create bvec and bval files for your B=0 series (e.g. https://github.com/rordenlab/spmScripts/...). Most DTI sequences have at least one B=0 image as well as the B-weighted images, so it should detect normal DTI scans fine. I would recommend setting up your DTI sequence to have a few B=0 images embedded with the weighted images, as this will improve measures like MD and DK (for my hints on DTI see here http://www.mccauslandcenter.sc.edu/crnl/...).
I tested my software on sequences from all vendors
https://www.nitrc.org/plugins/mwiki/index.php/dcm2nii:MainPage#Diffusion_Tensor_Imaging
But it is possible that your vendor has introduced its own private tags or methods to encode diffusion data. If so you can either provide sample images or create an updated version of dcm2niix that fixes the problem and submit a pull request on Github.
-c
Threaded View
Title | Author | Date |
---|---|---|
Graham Warner | Feb 3, 2017 | |
Chris Rorden | Feb 21, 2017 | |
Chris Rorden | Feb 3, 2017 | |