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Add curation script for INSPIRED dataset BIDSification #185

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wants to merge 38 commits into from
Closed

Add curation script for INSPIRED dataset BIDSification #185

wants to merge 38 commits into from

Commits on Nov 29, 2022

  1. Add python script for conversion of INSPIRED dataset to BIDS complian… 

    …t format
    @valosekj
    valosekj committed Nov 29, 2022
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  2. Implement MPM image BIDSification

    @valosekj
    valosekj committed Nov 29, 2022
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  3. Make sure that input args have abs path

    @valosekj
    valosekj committed Nov 29, 2022
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  4. Match also upper case in MPM json sidecars

    @valosekj
    valosekj committed Nov 29, 2022
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  5. Fix condition when there are no json sidecars for MPM images

    @valosekj
    valosekj committed Nov 29, 2022
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Commits on Nov 30, 2022

  1. Save conversion progress to log

    @valosekj
    valosekj committed Nov 30, 2022
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  2. Write participants.tsv file

    @valosekj
    valosekj committed Nov 30, 2022
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  3. Comments clarification

    @valosekj
    valosekj committed Nov 30, 2022
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Commits on Dec 2, 2022

  1. Create participants.json, dataset_description.json, and README files.… 

    … Copy the script itself to the path_output/code folder.
    @valosekj
    valosekj committed Dec 2, 2022
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Commits on Dec 4, 2022

  1. Use ISO-8859-1 encoding to open json files

    @valosekj
    valosekj committed Dec 4, 2022
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  2. Sort subjects in participants.tsv; fix typo in participants.json

    @valosekj
    valosekj committed Dec 4, 2022
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  3. Keep only .tar.gz subjects in the input dataset

    @valosekj
    valosekj committed Dec 4, 2022
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Commits on Dec 5, 2022

  1. Remove solved TODO

    @valosekj
    valosekj committed Dec 5, 2022
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  2. Add usage example

    @valosekj
    valosekj committed Dec 5, 2022
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Commits on Dec 12, 2022

  1. Remove function for automatic README creation.

    @valosekj
    valosekj committed Dec 12, 2022
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  2. Keep the original subjectID

    @valosekj
    valosekj committed Dec 12, 2022
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  3. Create .bidsignore to exclude bp-cspine tag from bids-validator

    @valosekj
    valosekj committed Dec 12, 2022
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  4. Fix bug in subject_id variable construction

    @valosekj
    valosekj committed Dec 12, 2022
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  5. Add README for inspired dataset

    @valosekj
    valosekj committed Dec 12, 2022
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Commits on Dec 21, 2022

  1. Switch from bp-cspine to acq-cspine

    @valosekj
    valosekj committed Dec 21, 2022
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  2. Deal with SC derivatives

    @valosekj
    valosekj committed Dec 21, 2022
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Commits on Jan 4, 2023

  1. Use label-SC_mask, label-WM_mask, and label-GM_mask

    @valosekj
    valosekj committed Jan 4, 2023
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  2. Include DatasetType (raw or derivative) to dataset_description.json. 

    Add write_json function.
    @valosekj
    valosekj committed Jan 4, 2023
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  3. Update participants.tsv and participants.json

    @valosekj
    valosekj committed Jan 4, 2023
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  4. Add script for merge of participants.tsv and table with clinical DCM … 

    …data
    @valosekj
    valosekj committed Jan 4, 2023
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  5. Rename data_id to source_id to be compatible with participants.tsv

    @valosekj
    valosekj committed Jan 4, 2023
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  6. Use n/a for empty cells

    @valosekj
    valosekj committed Jan 4, 2023
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  7. Add leading zeros to source_id and institution_id (to match with the … 

    …original participants.tsv)
    @valosekj
    valosekj committed Jan 4, 2023
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  8. Clarify script description

    @valosekj
    valosekj committed Jan 4, 2023
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Commits on Jan 6, 2023

  1. Rename derivatives/labels to derivatives/manual_labels

    @valosekj
    valosekj committed Jan 6, 2023
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Commits on Jan 20, 2023

  1. Copy qform to sform 

    To address spinalcordtoolbox/spinalcordtoolbox#3991 (comment)
    @valosekj
    valosekj committed Jan 20, 2023
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Commits on Jan 21, 2023

  1. Swap 'dir-AP_acq-cspine' to 'acq-cspine_dir-AP' to pass bids-validator

    @valosekj
    valosekj committed Jan 21, 2023
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  2. Change '_mask' to '_seg'

    @valosekj
    valosekj committed Jan 21, 2023
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  3. Rename README to README.md and update it.

    @valosekj
    valosekj committed Jan 21, 2023
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  4. Update 'participants.json' according to https://intranet.neuro.polymt… 

    …l.ca/data/dataset-curation.html#participants-json
    @valosekj
    valosekj committed Jan 21, 2023
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  5. README.md update

    @valosekj
    valosekj committed Jan 21, 2023
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Commits on Jan 24, 2023

  1. Move infolink 

    Co-authored-by: Julien Cohen-Adad <[email protected]>
    @valosekj @jcohenadad
    valosekj and jcohenadad authored Jan 24, 2023
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  2. Add Contact Person section 

    Co-authored-by: Julien Cohen-Adad <[email protected]>
    @valosekj @jcohenadad
    valosekj and jcohenadad authored Jan 24, 2023
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