From 1bafe035f58e07b17f144e33002f355458bdbf8a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jon=20Haitz=20Legarreta=20Gorro=C3=B1o?= Date: Fri, 20 Dec 2024 19:02:15 -0500 Subject: [PATCH] DOC: Miscellaneous improvements and fixes to the file format table Miscellaneous improvements and fixes to the file format table - Avoid adding an additional column and link to the format documentation using the names. - Fix the DICOM format extension: leave it to `none` and add a note about its most typical extension (`.dcm`). - Remove the unnecessary `nii.gz` and `mgh.gz` file extensions: add a note about cases where files have been compressed using an third-party tool (e.g. gzip). - Do not use third-party links for the NIfTI format: use the official NIfTI format webiste for its link. - Redirect to the DICOM format documentation instead of the general DICOM standard landing page. - Add Gordon Kindlmann as the origin/creator of the `NRRD` format. - Remove unnecessary whitespaces in cells. - Apply the changes to the table to the Jupyter notebook. --- code/01-scanner-to-computer.ipynb | 18 +++++++++++------- episodes/scanner-to-computer.md | 22 ++++++++++++---------- 2 files changed, 23 insertions(+), 17 deletions(-) diff --git a/code/01-scanner-to-computer.ipynb b/code/01-scanner-to-computer.ipynb index 58466e9..6de0045 100644 --- a/code/01-scanner-to-computer.ipynb +++ b/code/01-scanner-to-computer.ipynb @@ -11,13 +11,17 @@ "\n", "## Neuroimaging file formats\n", "\n", - "|Format Name | File Extension | Origin |\n", - "|---|---|---|\n", - "| DICOM | none | ACR/NEMA Consortium |\n", - "| Analyze | .img/.hdr | Analyze Software, Mayo Clinic |\n", - "| NIfTI | .nii | Neuroimaging Informatics Technology Initiative |\n", - "| MINC | .mnc | Montreal Neurological Institute |\n", - "| NRRD | .nrrd | |\n", + "| Format Name | File Extension | Origin/Group |\n", + "|-------------|----------------|--------------|\n", + "| [DICOM](https://www.dicomstandard.org/current) | none (*) | ACR/NEMA Consortium |\n", + "| [Analyze](https://eeg.sourceforge.net/ANALYZE75.pdf) | `.img`/`.hdr` | Analyze Software, Mayo Clinic |\n", + "| [NIfTI](https://nifti.nimh.nih.gov/) | `.nii` (**) | Neuroimaging Informatics Technology Initiative |\n", + "| [MINC](https://www.mcgill.ca/bic/software/minc) | `.mnc` | Montreal Neurological Institute |\n", + "| [NRRD](https://teem.sourceforge.net/nrrd/format.html) | `.nrrd` | Gordon L. Kindlmann |\n", + "| [MGH](https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat) | `.mgz` or `.mgh` | Massachusetts General Hospital |\n", + "\n", + "(*) DICOM files typically have a `.dcm` file extension.\n", + "(**) Some files are typically compressed and their extension may incorporate the corresponding compression tool extension (e.g. `.nii.gz`).\n", "\n", "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.\n", "\n", diff --git a/episodes/scanner-to-computer.md b/episodes/scanner-to-computer.md index 5228786..6b7b4c3 100644 --- a/episodes/scanner-to-computer.md +++ b/episodes/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.