JeffFessler / JeffFessler/mirt
mri_field_map_reg_scale causing bright pixels outside head
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- Dominant language
- MATLAB
- Stars
- 210
- Forks
- 76
- PR merge metrics
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Description
MH reports that putting images from J-SENSE recon code output
https://sigpy.readthedocs.io/en/latest/generated/sigpy.mri.app.JsenseRecon.html#sigpy.mri.app.JsenseRecon
into mri_field_map_reg.m causes amplification of pixels outside the head in this line:
https://github.com/JeffFessler/mirt/blob/43b20b5ea04b5bb61979aea7574ca73e3ea1b291/mri/fieldmap/mri_field_map_reg.m#L96
https://github.com/JeffFessler/mirt/blob/43b20b5ea04b5bb61979aea7574ca73e3ea1b291/mri/fieldmap/mri_field_map_reg.m#L148
Masking the fieldmaps (using ESPIRT masks) addressed the issue.
Fixing this is a low priority because I recommend using this code instead anyway:
https://github.com/ClaireYLin/regularized-field-map-estimation
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with mri/fieldmap/mri_field_map_reg.m at the referenced lines and reproduce the behavior using images from sigpy's JsenseRecon output. Compare the result with ESPIRT-masked fieldmaps; done means the reconstruction no longer amplifies pixels outside the head without requiring that masking workaround.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- matlab
- Domain
- computer-vision
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100