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updating to current status
1. The problem was that 1. all spin Echo has to have both AP and PA as Intended for 2. For whatever reason the Phase Encoding Directin comes out incorrect in the metatag for field maps, that is why we need this modification (both "j-" 3. In the future conversion to check if files that has Intended For exists or not.
THe code runs the ZHH classifier at 1 2 5 10 20 30 40 50 threshold in addition to HCP 10 threshold. Thsi will be build into amiklos/hcppipeline:4.11
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This would be a nice addition! |
Dockerfile.v5: - Base: Ubuntu 22.04 LTS (was Debian Jessie EOL) - HCP Pipelines: 5.0.0 from local copy (was 3.26.1 downloaded) - FreeSurfer: 7.3.2 (was 5.3.0-HCP) - FSL: 6.0.7.9 via fslinstaller (was 5.0.9) - Workbench: 1.5.0 (was 1.3.0) - Python: 3 via Miniconda3 (was Python 2) - pybids: >=0.15 (was 0.6.3) run.py: - Python 3 compatible (removed iteritems, from __future__, bytes decoding) - Updated pybids API: bids.grabbids -> bids, f.filename -> f.path, type= -> suffix=, extensions= -> extension= - nibabel API: get_header() -> header - Replaced removed layout.get_fieldmap() with custom get_fieldmap() helper that queries IntendedFor metadata directly Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
- Add libssl-dev, libcurl4-openssl-dev, libxml2-dev, libfontconfig1-dev, libfreetype6-dev for R package compilation (fs, sass dependencies) - Install party 1.0-25 dependencies (mvtnorm, modeltools, zoo, sandwich, strucchange, coin) explicitly before installing party_1.0-25 - Install core ICA-FIX packages after party to avoid dep resolution failures Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
coin >= 1.2 (2017) removed ExpectCovar/ExpectCovarInfluence from its namespace, breaking party_1.0-25 lazy loading. Install coin_1.1-3 from CRAN archive before installing party_1.0-25. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Large file (~10GB) was getting truncated mid-stream via wget pipe. Now requires freesurfer_linux-ubuntu22_amd64-7.3.2.tar.gz in build context (download with wget -c before building). Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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This implements ICA FIX. However in run.py line 370-375 modification was needed only for our site (was not reading this metatag correctly), so do not merge that (maybe a better way to do it).
ICA FIX was tested works fine with provided classifier on our HCP like data.