questions > How to process bruker DTI files
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Dec 21, 2022 10:12 AM | Palkin Arora - DRDO-INMAS
How to process bruker DTI files
Hi,
I am working on animal data using Bruker 7T. How to convert the files into nifti, I am trying to do using dcm2niix, latest version. But I am not getting .bval and .bvec files to process my data in DTI studio.
once I select the diacom folder the dcm2nifti window gets freeze into non responding state.
I am new to DTI studio, if possible can you help me with a pipeline for bruker DTI data processing in DTI studio.
I am working on animal data using Bruker 7T. How to convert the files into nifti, I am trying to do using dcm2niix, latest version. But I am not getting .bval and .bvec files to process my data in DTI studio.
once I select the diacom folder the dcm2nifti window gets freeze into non responding state.
I am new to DTI studio, if possible can you help me with a pipeline for bruker DTI data processing in DTI studio.
Dec 21, 2022 12:12 PM | Chris Rorden
RE: How to process bruker DTI files
This sounds like a duplicate of
https://github.com/rordenlab/dcm2niix/issues/525
https://github.com/rordenlab/dcm2niix/issues/265
The core issue is that the DICOM b-matrix 0018,9602..0018,9607 is underspecified to create a FSL bvec file (the bvec [1 0 0] and [-1 0 0] create identical bmatrixes, the theoretical diffusion is the same, but the eddy currents are not).
I have not seen a Broker scan in over a year, so it is possible they have fixed their DICOMs. Feel free to share your sample dataset with my institutional email:
https://sc.edu/study/colleges_schools/artsandsciences/psychology/our_people/directory/rorden_chris.php
However, my sense is that this is a limitation of your impoverished DICOM images, not dcm2niix. You should work with Bruker to ensure that archival data is created by your instrument.
https://github.com/rordenlab/dcm2niix/issues/525
https://github.com/rordenlab/dcm2niix/issues/265
The core issue is that the DICOM b-matrix 0018,9602..0018,9607 is underspecified to create a FSL bvec file (the bvec [1 0 0] and [-1 0 0] create identical bmatrixes, the theoretical diffusion is the same, but the eddy currents are not).
I have not seen a Broker scan in over a year, so it is possible they have fixed their DICOMs. Feel free to share your sample dataset with my institutional email:
https://sc.edu/study/colleges_schools/artsandsciences/psychology/our_people/directory/rorden_chris.php
However, my sense is that this is a limitation of your impoverished DICOM images, not dcm2niix. You should work with Bruker to ensure that archival data is created by your instrument.