# Anterior cingulate

See: {cite}`vogt1995human`.

Most brain hemispheres (65%) have a single *cingulate sulcus* delimited by
a *cingulate sulcus* above it:

![](images/vogt_1995_single_cs.png)

The rest have two cingulate sulci, with an extra *superior cingulate sulcus*
and *superior cingulate gyrus*:

![](images/vogt_1995_alternatives.png)

The cytoarchitectonic regions appear to correspond to the sulcal anatomy:

![](images/vogt_1995_cytoarchitecture.png)

## Match brain to template in high resolution

We are going to run the dipy non-linear registration to match a
high-resolution structural image to a high-resolution version of the template.

Then we're going to see what kind of job this does of matching anterior
cingulate anatomy to the template.

First, make sure you have these files in your working directory:

- `ds114_sub009_highres.nii`;
- `ds114_sub009_highres_brain_mask.nii`;
- `mni_icbm152_t1_tal_nlin_asym_09a.nii`;
- `mni_icbm152_t1_tal_nlin_asym_09a_mask.nii`;

You can do this by downloading the files one by one from the [Nipraxis-data
repository](https://github.com/nipraxis/nipraxis-data). Another, more automated
way of getting the files is using Nipraxis to fetch them from the web, then
copy the resulting files to your working directory.

```python
# Automatic download of data files to working directory.
from pathlib import Path
import shutil

import nipraxis

working_directory = Path()

for fname in ['ds114_sub009_highres.nii',
              'ds114_sub009_highres_brain_mask.nii',
              'mni_icbm152_t1_tal_nlin_asym_09a.nii',
              'mni_icbm152_t1_tal_nlin_asym_09a_mask.nii',
             ]:
    # Fetch the file
    local_fname = nipraxis.fetch_file(fname)
    # Copy to working directory
    shutil.copy2(local_fname, working_directory)
```

You should also download the {download}`dipy_registration.py` script file.

Have a look at `dipy_registration.py` for useful functions;

Now open IPython and:

```python
# In IPython (or Jupyter).
run dipy_registration.py
mapping = register_save('mni_icbm152_t1_tal_nlin_asym_09a.nii',
                        'mni_icbm152_t1_tal_nlin_asym_09a_mask.nii',
                        'ds114_sub009_highres.nii',
                        'ds114_sub009_highres_brain_mask.nii')
```

Leave that running - it will take something like 10-20 minutes depending on
your machine.  Meanwhile...

## Reviewing anatomy

We will be using [MRIcron](https://www.nitrc.org/projects/mricron):

-   [install MRIcron](https://people.cas.sc.edu/rorden/mricron/install.html).
-   review the help on how to [draw with
    MRIcron](https://people.cas.sc.edu/rorden/mricron/stats.html).
-   open the `ds114_sub009_highres.nii` file with MRIcron.  Scroll around the
    image, and have a look at the controls and menu items;
-   use the "View" menu "Display" option to switch to a display with larger
    versions of coronal, or axial or sagittal slices:

    ![](images/mricron_display.png)

-   what kind of cingulate anatomy (single, double) does this subject have in
    each hemisphere?  The sagittal slices might be most useful for that
    question;
-   make a new MRIcron window and open `mni_icbm152_t1_tal_nlin_asym_09a.nii`.
    You might want to play with the upper and lower image display thresholds to
    get good contrast in the image:

    ![](images/mricron_contrast.png)

- on a piece of paper, write down what you would like the registration to do
  to the subject's brain:

  - sketch the sulcal anatomy of the medial surface of each hemisphere for the
    subject and the template, as in the Vogt figure above;
  - do the same for the template image;
  - draw arrows from the subject hemisphere to the matching part of the
    template;

-   in MRIcron, use the "View, Display" to go to the *coronal* sections of the
    individual subject brain image;

-   find a coronal slice a little posterior to the genu of corpus callosum to
    start drawing:

    ![](images/mricron_draw.png)

    Have a look at [draw with mricron] for the drawing actions you will need
    using the keyboard and mouse.

-   using the diagram from the Vogt paper, draw your estimate for the position
    for left and right area 24 (a, b, c combined) on five adjacent
    slices through the anterior cingulate.  Click on the lower arrow of the y
    slice index at the top left to make sure you are moving in a posterior
    direction, one slice at a time:

    ![](images/mricron_y_scrolling.png)

- when you've finished drawing, use the y slice index arrow buttons to scroll
  through the image one slice at a time to make sure you haven't missed any
  slices, and you have drawn what you meant to;

- using the "Draw" menu in MRICron; "Save VOI" to save this definition in
  MRIcron's own format.  Add something like `_area_24` to the VOI name when
  saving;

- using the Draw menu "Convert" item, convert the VOI to a NIfTI file;

- if the registration has finished, open the new
  `w_ds114_sub002_highres.nii` file in MRIcron.  Compare it to the template,
  visually.  What do you think of the match?  How does it correspond to your
  drawing?

-   try loading the template image, and using the warped individual brain as an
    overlay:

    ![](images/mricron_overlays.png)

    Play with the overlay settings to get an idea of the quality of the
    registration;

- investigate the `dipy_registration.py` code for a useful function to
  resample the region definition file to the template voxel space.  Apply this
  function (or your own, if you prefer) to your region definition, to write out
  a version of the region image in template space;

- use the "Overlay" menu to load the resampled region on the:

  - template image;
  - resampled (warped) individual image;

  What do you think of the registration?  How does it compare to your drawing?
  Do you think the cytoarchitecture lines up with where you think it should be,
  given your drawing and the anatomy of the template and the individual subject
  image?

## References

```{bibliography}
:filter: docname in docnames
```