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DOC: Miscellaneous improvements and fixes to the file format table #55

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Dec 21, 2024
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DOC: Miscellaneous improvements and fixes to the file format table #55

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18 changes: 11 additions & 7 deletions code/01-scanner-to-computer.ipynb
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"\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",
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22 changes: 12 additions & 10 deletions episodes/scanner-to-computer.md
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### Anatomical

![](fig/t1t2flairbrain.jpg)

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 [image missing alt-text]: fig/t1t2flairbrain.jpg

*Sourced from [https://case.edu/med/neurology/NR/MRI%20Basics.htm](https://case.edu/med/neurology/NR/MRI%20Basics.htm)*

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### Functional

![](fig/bold.gif)

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 [image missing alt-text]: fig/bold.gif

![](fig/fmri_timeseries.png)

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 [image missing alt-text]: fig/fmri_timeseries.png

*Sourced from Wagner and Lindquist, 2015*

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### Diffusion

![](fig/dwi.gif)

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![](fig/dwi_tracts.png)

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 [image missing alt-text]: fig/dwi_tracts.png

*Sourced from [http://brainsuite.org/processing/diffusion/tractography/](https://brainsuite.org/processing/diffusion/tractography/)*

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<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.

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