Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Report BIDS PhaseEncodingDirection for 3D sequences #371

Closed
neurolabusc opened this issue Feb 3, 2020 · 1 comment
Closed

Report BIDS PhaseEncodingDirection for 3D sequences #371

neurolabusc opened this issue Feb 3, 2020 · 1 comment

Comments

@neurolabusc
Copy link
Collaborator

Historically, dcm2niix reported PhaseEncodingDirection for 2D sequences, as this information is commonly used to undistort 2D EPI images. However, these values were ignored for 3D sequences for two reasons: 1) dcm2niix will losslessly rotate 3D sequences as T1 (MP-RAGE) and T2 (SPACE) scans are often acquired as sagittal while 2D scans are acquired as axials (and slice timing does not impact 3D scans). 2.) Structural 3D scans have less spatial distortion that 2D EPI scans.

However, 3D EPI is becoming more common, so reporting these values may be useful. Particular care must be taken if the image is rotated, such that the reported axis is correctly reported.
neurolabusc added a commit that referenced this issue Feb 10, 2020
@neurolabusc
3D EPI TR (#369) 3D phase (#371) Enhanced ordering (#372 (comment))
96776fb
@neurolabusc
Copy link
Collaborator Author

Latest patch reports PhaseEncodingDirection for 3D EPI when it can be inferred.

yarikoptic added a commit to neurodebian/dcm2niix that referenced this issue May 6, 2020
@yarikoptic
Merge tag 'v1.0.20200331' into debian
c51c61e 
* tag 'v1.0.20200331': (52 commits)
  Update submodules
  Update dcm_qa submodule.
  UIH 3D sequence quirk
  New release, EstimatedTotalReadoutTime/EstimatedEffectiveEchoSpacing (rordenlab#377)
  Philips TotalReadoutTime (rordenlab#377)
  Cleanup
  Experimental Canon DICOM support (rordenlab#388)
  Experimental solution for issue 384 (rordenlab#384)
  Detect catastrophic anonymization (rordenlab#383)
  Only report "multiple inversion times" if 0018,9079 values differ (e.g. Bangalore data in https://github.com/neurolabusc/dcm_qa_philips)
  Consistent echo naming (rordenlab#381)
  Philips partial Fourier (rordenlab#377)
  Support InversionTImes (0018,9079) tag (rordenlab#380)
  Philips effective echo spacing formula ambiguous (rordenlab#377)
  TR for Philips 3D EPI (rordenlab#369)
  Citation (rordenlab#102)
  GE PET with variable slice intensity (rordenlab#374)
  Estimate Philips EffectiveEchoSpacing (nipreps/sdcflows#5)
  GE slice interpolation (rordenlab#373)
  3D EPI TR (rordenlab#369) 3D phase (rordenlab#371) Enhanced ordering (rordenlab#372 (comment))
  ...
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
1 participant
@neurolabusc