From 9dc6ae4d064e099751fb36dee0a2a519a23f9356 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Sat, 21 Dec 2024 00:05:16 +0000 Subject: [PATCH] differences for PR #55 --- md5sum.txt | 2 +- scanner-to-computer.md | 22 ++++++++++++---------- 2 files changed, 13 insertions(+), 11 deletions(-) diff --git a/md5sum.txt b/md5sum.txt index 1fe8d4e..96bc229 100644 --- a/md5sum.txt +++ b/md5sum.txt @@ -4,7 +4,7 @@ "config.yaml" "3ef23136064fd3627b556860c2d3040f" "site/built/config.yaml" "2024-02-18" "index.md" "78d2be0b54fef4ff7252449003cdc44f" "site/built/index.md" "2024-02-18" "episodes/before-we-start.md" "1e98940ca00552578a4e3b31e6064999" "site/built/before-we-start.md" "2024-02-18" -"episodes/scanner-to-computer.md" "4bfdc24a929fe0e133992bb995fdf4d4" "site/built/scanner-to-computer.md" "2024-12-20" +"episodes/scanner-to-computer.md" "d32d940876c7f2750198052618505e2d" "site/built/scanner-to-computer.md" "2024-12-21" "episodes/anatomy-of-nifti.md" "ac2a7fc719d8174b6d6274d7973a8d4b" "site/built/anatomy-of-nifti.md" "2024-02-29" "episodes/data-organization-bids.md" "0b88931c574033a6adad39c34fc340f9" "site/built/data-organization-bids.md" "2024-02-28" "episodes/open-mri-datasets.md" "9025db8aad6a5526209f349b43aa10c0" "site/built/open-mri-datasets.md" "2024-02-28" diff --git a/scanner-to-computer.md b/scanner-to-computer.md index 5228786..6b7b4c3 100644 --- a/scanner-to-computer.md +++ b/scanner-to-computer.md @@ -58,16 +58,18 @@ exercises: 10
Common file formats:
-| Format Name | File Extension | Origin/Group | More info| -| ----------- | -------------- | --------------------------------------------- |----------- -| DICOM | none or `.dc` | ACR/NEMA Consortium |https://www.dicomstandard.org/ | -| Analyze | `.img`/`.hdr` | Analyze Software, Mayo Clinic |https://eeg.sourceforge.net/ANALYZE75.pdf| -| NIfTI | `.nii` (or `.nii.gz`) | Neuroimaging Informatics Technology Initiative|https://brainder.org/2012/09/23/the-nifti-file-format/| -| MINC | `.mnc` | Montreal Neurological Institute |https://www.mcgill.ca/bic/software/minc| -| NRRD | `.nrrd` | |https://teem.sourceforge.net/nrrd/format.html| -| MGH |`.mgz` or `.mgh` (or `.mgh.gz`) | Massachusetts General Hospital|https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat| - - +| Format Name | File Extension | Origin/Group | +|-------------|----------------|--------------| +| [DICOM](https://www.dicomstandard.org/current) | none (*) | ACR/NEMA Consortium | +| [Analyze](https://eeg.sourceforge.net/ANALYZE75.pdf) | `.img`/`.hdr` | Analyze Software, Mayo Clinic | +| [NIfTI](https://nifti.nimh.nih.gov/) | `.nii` (**)| Neuroimaging Informatics Technology Initiative | +| [MINC](https://www.mcgill.ca/bic/software/minc) | `.mnc` | Montreal Neurological Institute | +| [NRRD](https://teem.sourceforge.net/nrrd/format.html) | `.nrrd` | Gordon L. Kindlmann | +| [MGH](https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat) | `.mgz` or `.mgh` | Massachusetts General Hospital | + +(*) DICOM files typically have a `.dcm` file extension. +(**) Some files are typically compressed and their extension may incorporate the corresponding +compression tool extension (e.g. `.nii.gz`). From the MRI scanner, images are initially collected in the DICOM format and can be converted to these other formats to make working with the data easier.