Comments (4)
@tundejunaid Is there a "PixelBandwidth"
field in your BIDS sidecar JSON for your T1 data? Also, what do you mean by "session not properly assigned in the BIDS data format"? Also, what scanner manufacturer is this data from? I hope I can help.
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I found out there was none and there are some other parameters not found like InPlanePhaseDirection and ParallelReductionPlane. And they seem really important for the structural analysis. I am using A Philipps scanner and I have no field map image. I am using this for my master thesis and any help or information would be appreciated.
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@tundejunaid I would talk to whoever is closest to the MRI acquisition data and ask them for whatever the Philips equivalent of a Siemens "protocol PDF" is for acquisition timing parameters and the like. You will likely need a few of those fields inserted into your BIDS sidecar JSONs for processing. If you determine these fields unnecessary for your processing needs, then we can consider making a change to this application to accommodate unnecessary fields.
You may also want to consider satisfying the official BIDS validator for pristine input data before trying to process.
https://github.com/bids-standard/bids-validator#quickstart
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All is working fine, I think the problem was the first dataset I tried it with. the conversion to BIDS was not from the DICOM but from a REC File. When I tried with another Data converted From DICOM it was all good
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Related Issues (20)
- Support for FLAIR option as in original HCP
- Stuck at FreeSurfer Stage (mris_fix_topolo) HOT 2
- Major pipelines.py bugs in Stage.remove_expected_outputs and PreFreeSurfer._get_intended_sefmaps
- Remove planned-but-never-implemented pipelines.py functionality
- swarm/cloud v0.1.0 HOT 1
- Exception: error caught during stage: DCANBOLDProcessing HOT 4
- nonlin masking error HOT 1
- dataset_description.json HOT 14
- Request for task-residualized data HOT 5
- t1 json - missing PixelBandwidth? HOT 2
- Clarification for filtered timeseries dtseries and mask data HOT 4
- padding fix for bandpass filtering in DCAN BOLD of dcanumn/abcd-hcp-pipeline not working correctly HOT 1
- segmentation error HOT 3
- Respiration filter recommendations for TR greater than 1? HOT 3
- Exception: error caught during stage: FMRIVolume HOT 1
- Grab Readout Dir from a more intuitive JSON field
- Add filemapper as pipeline stage to automatically generate derivates HOT 1
- Possible ants bracket expansion bug
- StudyTemplate fails at PostFreeSurfer HOT 2
- Commit to Readthedocs, remove readme
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