lh
rh
midline
and mixed
. The structure of your directory should be like this:STN_lh.nii.gz
is not necessary. This is especially not intended, if the same structure appears in both lh
and rh
subfolders. In that case, the filenames should be identical. Place structures that exist only once in the brain (such as the hypophysis) or midline structures (like the fornix) into the midline
subfolder. In case you have one NIfTI file for a bilateral structure (such as one file showing left and right STN) into the mixed
subfolder.Render 3D
and press Run
. The first run takes long, be patient. The reason is that Lead-DBS needs to aggregate all information into a single file (atlas_index.mat
) and creates a gray matter mask for VTA calculations (gm_mask.nii.gz
).labeling
atlas and then use the ea_labeling2atlas
function to convert the file into a Lead-DBS atlas.labeling
into an atlas, now runea_labeling2atlas('my_atlas');
/atlases
subdirectory. Usually, you can delete the .nii and .txt files from the /labeling
folder after converting them to an atlas.Render 3D
and press Run
. The first run takes long, be patient. The reason is that Lead-DBS needs to aggregate all information into a single file (atlas_index.mat
) and creates a gray matter mask for VTA calculations (gm_mask.nii.gz
).ea_atlas2labeling
function, as well. However, be aware that since the two formats have different capabilities and limitations, converting from one to the other isn't always straight-forward and results should be carefully checked.ea_atlas.index
and gm_mask.nii.gz
. The former can be modified (using MATLAB) to change colors of the atlas or to group entries to "presets" that can be easily toggled on or off. For instance, you may take a closer look on the DISTAL (Ewert 2017)
in the 3D viewer to understand what possibilities are there. In the Atlas control figure, you can choose useful presets to visualize (such as Primary DBS targets
. By choosing either STN: Solid
or STN: Subzones
the STN will be shown as a single structure or divided into motor, associative or limbic functional domains.atlas_index.mat
file of the DISTAL atlas into MATLAB:atlases.defaultset
). The "default" entry can be absolute
(meaning the preset will only show structures defined in the show
entry and hide structures defined in the hide
field) or relative
(in which case the currently visible set of structures will not be altered if not explicitly mentioned).atlases.colors
fields and the colormap to use by adding an atlases.colormap
field (if not already present). For instanceatlases.colors
ascendingly from red over white to blue.