diff --git a/_sources/data/dataset-curation.md b/_sources/data/dataset-curation.md index ef5a4686..0e497ac0 100644 --- a/_sources/data/dataset-curation.md +++ b/_sources/data/dataset-curation.md @@ -120,6 +120,9 @@ An alphanumeric string located after all the entities following a final undersco Only **ONE** suffix can be used within the filename. +```{note} +For localizer/scout images, you can use `_acq-localizer_T1w.nii.gz`. (Relevant discussion [here](https://github.com/neuropoly/data-management/issues/325#issuecomment-2186894284) and [here](https://neurostars.org/t/how-to-name-localizer-scans-in-bids/29720/2).) +``` ### Raw extensions diff --git a/data/dataset-curation.html b/data/dataset-curation.html index 62c6f6b0..acd44dc7 100644 --- a/data/dataset-curation.html +++ b/data/dataset-curation.html @@ -597,6 +597,10 @@

Raw suffixes +

Note

+

For localizer/scout images, you can use <entities>_acq-localizer_T1w.nii.gz. (Relevant discussion here and here.)

+

Raw extensions#

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"AWS": [[59, "aws"]], "Abstracts": [[20, "abstracts"]], "Access from stations": [[26, "access-from-stations"]], "Access to UNF": [[80, "access-to-unf"]], "Accessing Datasets (external volumes)": [[55, "accessing-datasets-external-volumes"]], "Account Creation": [[14, "account-creation"]], "Acknowledgements": [[110, "acknowledgements"]], "Acquisition": [[75, "acquisition"]], "Add LINUX machine to GRAMES ": [[84, "add-linux-machine-to-grames"]], "Add PolyMTL email to the macOS Mail app": [[86, "add-polymtl-email-to-the-macos-mail-app"]], "Add SSH key": [[39, "add-ssh-key"]], "Add tag": [[39, "add-tag"]], "Addressing Reviewer Comments": [[110, "addressing-reviewer-comments"]], "Admin": [[15, "admin"]], "Admin guide for data.neuro.polymtl.ca": [[27, "admin-guide-for-data-neuro-polymtl-ca"]], "Admission at Polytechnique": [[22, "admission-at-polytechnique"]], "Advanced Normalization Tools (ANTs)": [[42, "advanced-normalization-tools-ants"]], "Affiliation with Mila": [[82, 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[[31, "compression-extraction"]], "Computer Setup": [[83, "computer-setup"]], "Computer Vision": [[22, "computer-vision"]], "Computers": [[92, "computers"], [99, "computers"]], "Concordia (3T GE)": [[77, "concordia-3t-ge"]], "Conditional Random Fields (CRF)": [[34, "conditional-random-fields-crf"]], "Configure git": [[39, "configure-git"]], "Configure virtualenvwrapper under LINUX ": [[84, "configure-virtualenvwrapper-under-linux"]], "Connect to NeuroPoly Computers": [[15, "connect-to-neuropoly-computers"]], "Connect to Windows Servers": [[15, "connect-to-windows-servers"]], "Connect to the Polytechnique public disk": [[15, "connect-to-the-polytechnique-public-disk"]], "Connecting": [[17, "connecting"]], "Connecting from the command-line (cloning a repo)": [[28, "connecting-from-the-command-line-cloning-a-repo"]], "Connecting to the web interface": [[28, "connecting-to-the-web-interface"]], "Connection closed by remote host": [[39, "connection-closed-by-remote-host"]], "Connectors": [[99, "connectors"]], "Consultant": [[89, "consultant"]], "Consultants and RA": [[89, "consultants-and-ra"]], "Continual Learning": [[3, "continual-learning"]], "Continuous Integration": [[94, "continuous-integration"]], "Contribute to a project": [[39, "contribute-to-a-project"]], "Converting data to BIDS": [[24, "converting-data-to-bids"]], "Copy (and synchronize) with rsync": [[31, "copy-and-synchronize-with-rsync"]], "Copy file between computers": [[31, "copy-file-between-computers"]], "Copy file into container ": [[54, "copy-file-into-container"]], "Copy from a remote station": [[31, "copy-from-a-remote-station"]], "Copy from remote station via scp": [[31, "copy-from-remote-station-via-scp"]], "Copy/Make a disk image from CD/DVD (ISO format) ": [[67, "copy-make-a-disk-image-from-cd-dvd-iso-format"]], "Copying": [[31, "copying"], [31, "id2"]], "Courses and Tutorials": [[73, "courses-and-tutorials"]], "Courses:": [[39, "courses"]], "Cover letter": [[110, "cover-letter"]], "Create 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"histology"]], "How to always open a page with \u201cpage width\u201d view ": [[58, "how-to-always-open-a-page-with-page-width-view"]], "How to design PCB for PCBWAY ": [[108, "how-to-design-pcb-for-pcbway"]], "How to design PCB for Poly-Grames": [[108, "how-to-design-pcb-for-poly-grames"]], "How to merge specific files from another branch": [[39, "how-to-merge-specific-files-from-another-branch"]], "How to use XCode toolchain as a non-admin user?": [[71, "how-to-use-xcode-toolchain-as-a-non-admin-user"]], "I heard that the WiFi is changing? Could this affect my access?": [[85, "i-heard-that-the-wifi-is-changing-could-this-affect-my-access"]], "IDEs": [[73, "ides"]], "IEEE EMBS ISC": [[20, "ieee-embs-isc"]], "IF - AND": [[32, "if-and"]], "IF - OR": [[32, "if-or"]], "IF Statements": [[32, "if-statements"]], "ISBI": [[20, "isbi"]], "ISMRM": [[20, "ismrm"]], "ITK Transform File": [[42, "itk-transform-file"]], "ITK-SNAP": [[48, "itk-snap"]], "Ignore file mode": [[39, "ignore-file-mode"]], "Image Capture": [[67, "image-capture"]], "Image Processing": [[7, "image-processing"]], "Image Processing Software": [[41, "image-processing-software"]], "Import a .ova file ": [[63, "import-a-ova-file"]], "Informatics": [[95, "informatics"]], "Infrastructure": [[92, "infrastructure"]], "Initial setup": [[28, "initial-setup"]], "Install & Run Linux distribution ": [[54, "install-run-linux-distribution"]], "Install ITK": [[70, "install-itk"]], "Install VTK": [[70, "install-vtk"]], "Install git": [[39, "install-git"]], "Install guest additions 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"Recipe from UNF": [[107, "recipe-from-unf"]], "Recommendations ": [[44, "recommendations"]], "Reconstruct raw data": [[80, "reconstruct-raw-data"]], "Recover lost commits after rebase": [[39, "recover-lost-commits-after-rebase"]], "Recovery": [[67, "recovery"]], "Recovery Shortcut": [[27, "recovery-shortcut"]], "Reduce the size of the VM ": [[63, "reduce-the-size-of-the-vm"]], "Reference": [[35, "reference"]], "Reference ": [[38, "reference"]], "Reference manager": [[110, "reference-manager"]], "References": [[14, "references"]], "Reimbursement": [[20, "reimbursement"]], "Reimbursements": [[99, "reimbursements"]], "Releases": [[27, "releases"]], "Remove Docker image or containers (force deletion) ": [[54, "remove-docker-image-or-containers-force-deletion"]], "Remove Tag": [[39, "remove-tag"]], "Remove a branch": [[39, "remove-a-branch"]], "Remove files from tmp ": [[31, "remove-files-from-tmp"]], "Rename files with a given extension": [[31, "rename-files-with-a-given-extension"]], "Renaming": [[31, "renaming"]], "Requirements for Polytechnique": [[22, "requirements-for-polytechnique"]], "Requirements for room access": [[82, "requirements-for-room-access"]], "Research Associates": [[89, "research-associates"]], "Reset Commit": [[39, "reset-commit"]], "Reset your branch (revert your local commits)": [[39, "reset-your-branch-revert-your-local-commits"]], "Resetting": [[40, "resetting"]], "Resources": [[4, "resources"], [72, "resources"], [73, "resources"]], "Restrict Gradient Deformation": [[42, "restrict-gradient-deformation"]], "Restricted Boltzmann Machines (RBM)": [[37, "restricted-boltzmann-machines-rbm"]], "Retrieve an old backup": [[15, "retrieve-an-old-backup"]], "Reviewers": [[94, "reviewers"]], "Right-click sharing for Google Drive": [[67, "right-click-sharing-for-google-drive"]], "Rods": [[99, "rods"]], "Rollbacks": [[39, "rollbacks"]], "Run Docker image ": [[54, "run-docker-image"]], "Run with DISPLAY redirection ": [[54, "run-with-display-redirection"]], "Running MacOS ": [[62, "running-macos"]], "Running Remotely": [[47, "running-remotely"]], "SFTP (Mount a remote station)": [[15, "sftp-mount-a-remote-station"]], "SSH": [[64, "ssh"]], "SSH (command line)": [[15, "ssh-command-line"]], "SSH Public Key": [[31, "ssh-public-key"]], "SSH into Box ": [[62, "ssh-into-box"]], "SSH tunnelling": [[17, "ssh-tunnelling"]], "Save a Docker image ": [[54, "save-a-docker-image"]], "Scheduled reboots": [[15, "scheduled-reboots"]], "Sci-Kit Learn Tools ": [[37, "sci-kit-learn-tools"]], "Screen (for background processes)": [[31, "screen-for-background-processes"]], "Screenshot in desired format ": [[67, "screenshot-in-desired-format"]], "Script": [[32, "script"]], "Search file name": [[39, "search-file-name"]], "Search for remote image": [[54, "search-for-remote-image"]], "Segmentation": [[9, "segmentation"]], "Select default branches for pushing": [[39, "select-default-branches-for-pushing"]], "Servers": [[67, 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