bidskit
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jmtyszka
Utility functions for working with DICOM and BIDS neuroimaging data
It would be nice to include an option that tells bidskit perform some checks to make sure that the Protocol_Translator.json file is compatible with BIDS naming rules. For example: 1....
Currently, the --bind-fmaps flag populates the IntendedFor fields in the fmap/*.json files with the fieldmap(s) closest in time to the start of each BOLD series. Because our fieldmaps are collected...
We have participants.tsv produced, but not a scans.tsv for each session. I personally believe the information in this file is a bit redundant, since it can all be found in...
**Is your feature request related to a problem? Please describe.** A clear and concise description of what the problem is. Ex. I'm always frustrated when [...] BIDSKIT works great and...
Hi, I am trying to run the latest version of bidskit (2022.10.4) but am getting a key error for `SerDesc` during the second pass (output below). ``` ------------------------------------------------------------ Pass 2...
Hi, I am new to resting state fMRI. First of all, thank you for this, it certainly is a useful tool. I am working with an online dataset PPMI from...
**Describe the bug** The docs mention "Protocol_Translator.json" as necessary for the BIDS conversion, but there is not a detailed specification of this file in `bidskit`, BIDs starter-kit or the BIDS...
**Describe the bug** Using Python 3.6, 3.9, and 3.12.1, I have not been able to use `bidskit` (installed through pip). Any usage of the module gives the error, "TypeError: Expected...
When running bidskit for the second time using the following command, `bidskit -d {data_dir} -subj {subjects_to_convert} -sess {sessions_to_convert}` the file `participants.json` and `dataset_description.json` are overwritten, even if I've set them...
**Describe the bug** For CT Scan Dicoms that have tilt correction, *.json sidecar is not created. Hence, an error prevents dcm2niix and bidskit from continuing. **To Reproduce** Unfortunately, I cannot...