Merge pull request #55 from jhlegarreta/MiscFileFormatTableFixes

DOC: Miscellaneous improvements and fixes to the file format table
carpentries-incubator · Dec 21, 2024 · 3c16073 · 3c16073
2 parents 659646a + 1bafe03
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diff --git 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
@@ -58,16 +58,18 @@ exercises: 10
 
 <h6 id="fileformats"> Common file formats:</h6>
 
-| 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.