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added myelin map to docs #179

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Apr 1, 2022
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added myelin map to docs #179

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11 changes: 9 additions & 2 deletions docs/tutorials/outputs.md
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Expand Up @@ -23,12 +23,12 @@ In this example, a `T1w` image was used as a standard reference image, but a `T2
   ├── sub-001_desc-preproc_T1w.nii.gz
   ├── sub-001_space-T1w_desc-preproc_T2w.nii.gz
   ├── sub-001_hemi-R_space-T1w_desc-subfields_dseg.nii.gz
   ├── sub-001_space-cropT1w_desc-preproc_T2w.nii.gz
   ├── sub-001_hemi-R_space-cropT1w_desc-preproc_T2w.nii.gz
   └── sub-001_hemi-R_space-cropT1w_desc-subfields_dseg.nii.gz

As per BIDS guidelines, `desc-preproc` refers to preprocessed input images, `space-T1w` refers to the volume to which the image is registered, `hemi` refers to the left or right hemisphere (only shown for the right in this example), and`desc-subfields_dseg` images contains subfield labels (coded as integers as described in the included `volumes.tsv` file). Note that HippUnfold does most intermediate processing in an unshown `space-corobl` which is cropped, upsampled, and rotated. Downsampling to the original `T1w` space can thus degrade the results and so they are also provided in a higher resolution `space-cropT1w` space which is ideal for conducting volumetry or morphometry measures with high precision and detail.

For example, the following Image shows a whole-brain `T1w` image, a
For example, the following image shows a whole-brain `T1w` image, a
`space-cropT1w` overlay of the upsampled T2w image (centre square), and a similarly upsampled output
subfield segmentation (colour).

Expand Down Expand Up @@ -118,6 +118,13 @@ Note that the dentate uses the same unfolding methods as the rest of the hippoca

Corresponding `coords` and `warp` files are also generated.

### New: myelin maps


If your dataset has T1w and T2w images (and you are using `--modality=T1w` or `--modality=T2w`), then you can enable the generation of myelin maps as the ratio of T1w over T2w images. This division is done in the `corobl` space, and provides `myelin.shape.gii` surface metrics, and also includes these in the CIFTI and spec files.

This option is enabled with the `--generate-myelin-maps` command-line option.

## coords

Hippunfold also provides images that represent anatomical gradients
Expand Down