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Centre Hospitalier Universitaire Vaudoise
- Lausanne, Switzerland
- @oesteban
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nipype
nipype PublicForked from nipy/nipype
Workflows and interfaces for neuroimaging packages
Python
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mriqc
mriqc PublicForked from nipreps/mriqc
The package provides a series of image processing workflows to extract and compute a series of NR (no-reference), IQMs (image quality metrics) to be used in QAPs (quality assessment protocols) for …
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2,185 contributions in the last year
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Activity overview
Contribution activity
November 2023
Created 132 commits in 9 repositories
Created 3 repositories
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oesteban/phys2cvr
Python
This contribution was made on Nov 22
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oesteban/talks
HTML
This contribution was made on Nov 16
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oesteban/pyedfread
Cython
This contribution was made on Nov 10
Created a pull request in TheAxonLab/hcph-sops that received 11 comments
ENH: Alternative implementation to events files with Pandas
Reusing some of the foundations from #272 this PR adds the code to generate events files from Psychopy. Alongside the PR, the data repository has b…
Opened 27 other pull requests in 5 repositories
TheAxonLab/hcph-sops
17
merged
1
open
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ENH: Add *PyBIDS*' indexing and address BIDS-Validator errors
This contribution was made on Nov 28
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ENH: Add a jupyter notebook for consolidation of metadata
This contribution was made on Nov 28
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ENH: Add sessions 47 and 48
This contribution was made on Nov 17
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ENH: Add sessions 43-46 (physio and events)
This contribution was made on Nov 14
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ENH: Reduce storage hunger by gzipping the original DICOMS
This contribution was made on Nov 13
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ENH: Add schedules for sessions 39 through 42
This contribution was made on Nov 12
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ENH: Refactor ET to BIDS conversion into a Jupyter notebook
This contribution was made on Nov 10
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ADD: sessions 37 and 38 (physio and events)
This contribution was made on Nov 10
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ENH: More specific tear-down details, recognizing recent events
This contribution was made on Nov 10
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FIX: Minor details about ET to BIDS conversion
This contribution was made on Nov 10
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ENH: Update session table with make-up sessions
This contribution was made on Nov 9
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ENH: Include QA/QC of unprocessed data
This contribution was made on Nov 8
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ENH: Revise respiration belt information with more details
This contribution was made on Nov 6
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ENH: Add session 29 and update notebook for sessions with missing RB
This contribution was made on Nov 4
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ENH: Add physiological recordings of session 28
This contribution was made on Nov 4
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ENH: Update physio conversion with sessions 25 & 26
This contribution was made on Nov 2
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FIX: Rendering of
$$
latex environmentThis contribution was made on Nov 1 -
FIX: Revise tear-down protocol and remove outdated steps
This contribution was made on Nov 1
nipreps/mriqc
4
merged
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Update bold to large resource class in config.yml
This contribution was made on Nov 17
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ENH: Large overhaul of the functional workflow w/focus on ME-EPI
This contribution was made on Nov 15
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ENH: Implement BIDS filters file and drop legacy BIDS querying
This contribution was made on Nov 14
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ENH: Swap background and zoomed-in visualizations in anatomical reports
This contribution was made on Nov 13
nipreps/sdcflows
1
open
1
merged
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ENH: Standalone CLI now estimates fieldmaps
This contribution was made on Nov 28
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FIX: Wrangler now ignores
part-phase
EPI filesThis contribution was made on Nov 28
nipy/nitransforms
2
merged
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FIX: Postpone coordinate mapping on linear array transforms
This contribution was made on Nov 16
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FIX: Inefficient iterative reloading of reference and moving images
This contribution was made on Nov 16
nipreps/niworkflows
1
merged
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FIX: Add DWI to the default queries of BIDS querying
This contribution was made on Nov 14
Reviewed 29 pull requests in 9 repositories
TheAxonLab/hcph-sops
17 pull requests
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Enh/edf2bids notebook
This contribution was made on Nov 29
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ENH: Add
events.tsv
to the post-scanner flowchartThis contribution was made on Nov 28 -
ENH: document QC checkpoint after denoising
This contribution was made on Nov 28
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FIX: bug preventing the generation of events.tsv for resting-state
This contribution was made on Nov 28
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ENH: Add tests for events files
This contribution was made on Nov 28
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FIX: physio to BIDS conversion
This contribution was made on Nov 28
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FIX: MRIQC and datalad
This contribution was made on Nov 27
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fix: filenames in schedule.tsv
This contribution was made on Nov 23
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ENH: Include QA/QC of unprocessed data
This contribution was made on Nov 22
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ENH: Add post-scanner data flowchart
This contribution was made on Nov 22
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ENH : Update the SOPs specifying the ET-to-BIDS conversion
This contribution was made on Nov 8
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ENH: Describe execution of MRIQC and how to add the derivatives
This contribution was made on Nov 8
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ENH: Conversion of ET messages into BIDS (with bidsphysio)
This contribution was made on Nov 7
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ENH: Alternative implementation to events files with Pandas
This contribution was made on Nov 6
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WIP: generate events.tsv from psychopy log
This contribution was made on Nov 6
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FIX: Revise tear-down protocol and remove outdated steps
This contribution was made on Nov 1
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ENH: Conversion from *AcqKnowledge* to BIDS
This contribution was made on Nov 1
nipy/nitransforms
3 pull requests
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output displacement fields
This contribution was made on Nov 17
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FIX: Postpone coordinate mapping on linear array transforms
This contribution was made on Nov 16
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FIX: Inefficient iterative reloading of reference and moving images
This contribution was made on Nov 16
nipreps/mriqc
2 pull requests
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ENH: Large overhaul of the functional workflow w/focus on ME-EPI
This contribution was made on Nov 18
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ENH: Implement BIDS filters file and drop legacy BIDS querying
This contribution was made on Nov 15
nipreps/niworkflows
2 pull requests
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RF: Replace Convert3d with nitransforms in MCFLIRT2ITK
This contribution was made on Nov 17
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FIX: Add DWI to the default queries of BIDS querying
This contribution was made on Nov 14
nipreps/sdcflows
1 pull request
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ENH: Resolve BIDS-URIs
This contribution was made on Nov 28
bids-standard/bids-specification
1 pull request
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[ENH] BEP 020 Eye Tracking
This contribution was made on Nov 28
nipreps/fmriprep
1 pull request
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fMRIPrep 23.2.0alpha
This contribution was made on Nov 21
TheAxonLab/HCPh-fMRI-tasks
1 pull request
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DOC: detailed description of QCT
This contribution was made on Nov 10
bids-standard/bids-extensions
1 pull request
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first draft of general conventions page
This contribution was made on Nov 7
Created an issue in bids-standard/pybids that received 7 comments
Fieldmaps do not find metadata when part-{mag,phase}
are present and a single sidecar is given
I have:
sub-001/ses-001/fmap/sub-001_ses-001_acq-bold_dir-AP_epi.json
sub-001/ses-001/fmap/sub-001_ses-001_acq-bold_dir-AP_part-mag_epi.nii.gz
sub-…
Opened 16 other issues in 3 repositories
TheAxonLab/hcph-sops
10
open
3
closed
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_eyetrack.json
wrongly defineStartTime
andStopTime
This contribution was made on Nov 9 -
Write physio QC procedures and criteria
This contribution was made on Nov 8
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QA/QC protocol for preprocessed data
This contribution was made on Nov 8
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QA/QC protocol for unprocessed data
This contribution was made on Nov 8
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ET: Convert all sessions to BIDS
This contribution was made on Nov 8
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Create a Jupyter notebook demonstrating ET conversion into BIDS
This contribution was made on Nov 8
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Add the first session of ET data in BIDS to the dataset
This contribution was made on Nov 8
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Rewrite ET-to-BIDS conversion in the SOPs
This contribution was made on Nov 8
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Include ET "messages" within the BIDS distribution of the dataset
This contribution was made on Nov 7
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Consider unit tests on code generating events files and physio
This contribution was made on Nov 7
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Transfer QC checks on events files from WIP PR
This contribution was made on Nov 6
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Deep revision of physio of session 4
This contribution was made on Nov 1
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Convert physio to BIDS - sessions 11 and 13
This contribution was made on Nov 1
nipreps/mriqc
2
closed
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Aggregate all echoes of multi-echo fMRI in a single report
This contribution was made on Nov 13
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[Report] Move background visualization of anatomical images up above the zoomed-in view of the brain
This contribution was made on Nov 13
Medical-Image-Analysis-Laboratory/fetal_brain_qc
1
closed
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License is missing
This contribution was made on Nov 9