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first try #54

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Dec 20, 2024
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first try #54

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19 changes: 12 additions & 7 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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![](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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*Sourced from [http://brainsuite.org/processing/diffusion/tractography/](https://brainsuite.org/processing/diffusion/tractography/)*

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## Neuroimaging file formats

| Format Name | File Extension | Origin |
| ----------- | -------------- | ---------------------------------------------- |
| DICOM | none | ACR/NEMA Consortium |
| Analyze | .img/.hdr | Analyze Software, Mayo Clinic |
| NIfTI | .nii | Neuroimaging Informatics Technology Initiative |
| MINC | .mnc | Montreal Neurological Institute |
| NRRD | .nrrd | |
<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|



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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