https://wiki.mrrc.pitt.edu/ 2026-06-04T23:46:10+00:00 https://wiki.mrrc.pitt.edu/ https://wiki.mrrc.pitt.edu/lib/exe/fetch.php?media=wiki:dokuwiki.svg text/html 2026-06-03T18:01:39+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.mrrc.pitt.edu/doku.php?id=npac:internal_weekly&rev=1780509699&do=diff NPAC Internal Weekly Notes * Zoom * Prev (20241107 - 20250820) tetra confluence Elijah 50% Will 30% Andrew 10% Format Notes: - enumerate list w/~ 1h time spend * unordered bullet w/ | 1h time estimate ideally: link to git diff (compare/main~3..main) & link to wiki page. text/html 2026-04-15T18:53:24+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.mrrc.pitt.edu/doku.php?id=npac:mp2rage&rev=1776279204&do=diff MP2RAGE The MP2RAGE acquisition uses two inversions to create a UNIT1 T1w-like image. In BIDS, this would look like sub-12199/ses-1ptx/anat/ ├── sub-12199_ses-1ptx_inv-1_MP2RAGE.json ├── sub-12199_ses-1ptx_inv-1_MP2RAGE.nii.gz ├── sub-12199_ses-1ptx_inv-2_MP2RAGE.json ├── sub-12199_ses-1ptx_inv-2_MP2RAGE.nii.gz ├── sub-12199_ses-1ptx_UNIT1.json └── sub-12199_ses-1ptx_UNIT1.nii.gz text/html 2025-09-26T15:06:23+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.mrrc.pitt.edu/doku.php?id=npac:nda&rev=1758899183&do=diff National Data Archive (NIH NDA) Imaging Upload NIH grants require datasharing, many to <https://nda.nih.gov/>. Imaging data can be tricky to upload. A BIDS organized dataset can be converted to the image03 “Expected Data” input type and uploaded with nda-tools's vtcmd with minimal intervention. See text/html 2026-04-15T17:40:29+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.mrrc.pitt.edu/doku.php?id=npac:neuromelanin&rev=1776274829&do=diff Neuromelanin Tech agreement with Columbia University Tech Ventures (Cassidy, Horga, Wengler). * <https://github.com/LabNeuroCogDevel/NM_toolbox> * <https://lncd.pitt.edu/wiki/doku.php?id=tools:neuromelanin> Wengler et al., NeuroImage. 2020; 208:116457. All rights reserved. Kenneth Wengler @ CU, NYSPI 2019 Portions of this toolbox were adapted from the ASLtbx: Ze Wang @ TRC, CFN, Upenn 2004. Portions of this toolbox were adapted from code by Clifford Cassidy @ CU, NYSPI, 2018. This toolb… text/html 2026-05-19T17:29:40+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.mrrc.pitt.edu/doku.php?id=npac:qc&rev=1779211780&do=diff Phantom QC This is the development page for results on Daily Scanner Quality Control (one of QA Overview) <https://github.com/NPACore/fw-mrrcqa> Components: * EPI: Z-Shim Value QC tSNR * Channels: FID * TTL trigger: TTL (TTL BNC, Triggering Task Start) Automation The pipeline is convoluted and distributed: * flywheel gear rules submmit QC jobs * FID FWHM is a file-curate gear ( text/html 2026-04-15T17:36:53+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.mrrc.pitt.edu/doku.php?id=npac:support&rev=1776274613&do=diff NPAC Support and Services The Neuroimaging Processing and Analytics Core can support * Organizing imaging data * scheduled and automatic BIDS-ificiation (ReproIn) * unattended REDCap integration * Flywheel on-boarding * gear rule setup gearules * gear development support Flywheel Gears * Scripting text/html 2024-09-26T15:32:04+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.mrrc.pitt.edu/doku.php?id=npac:wishlist&rev=1727364724&do=diff * flywheel * project testing/configuring * PI onboarding * REDCap integration * HPC integration * BIDS-ify+containerizing pipelines * ChanMoon QA code * tat2, r2prime, neuromelanin, hallquist's preprocess_functional * National data archive (NDA) upload/share automation text/html 2026-04-29T13:57:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://wiki.mrrc.pitt.edu/doku.php?id=npac:xnat&rev=1777471053&do=diff XNAT Automation * <https://wiki.xnat.org/documentation/using-the-xnat-event-service> Custom data * <https://wiki.xnat.org/documentation/adding-custom-variables-to-xnat-projects>