Metadata-Version: 2.5
Name: fw-gear-ants-dbm-longitudinal
Version: 0.1.2
Summary: Run ANTs antsLongitudinalCorticalThickness.sh script
Project-URL: Repository, https://gitlab.com/flywheel-io/scientific-solutions/gears/ants-dbm-longitudinal
Author-email: Flywheel <support@flywheel.io>
License-Expression: MIT
License-File: LICENSE
Keywords: Flywheel,Gears
Classifier: Topic :: Scientific/Engineering
Requires-Python: ~=3.12
Requires-Dist: backoff>=2.2.1
Requires-Dist: flywheel-gear-toolkit>=0.6.22
Requires-Dist: flywheel-sdk>=21.6.1
Requires-Dist: joblib>=1.5.3
Requires-Dist: matplotlib>=3.10.9
Requires-Dist: nipype>=1.11.0
Requires-Dist: pandas>=3.0.2
Requires-Dist: psutil>=7.2.2
Description-Content-Type: text/markdown

# ANTs DBM Longitudinal

A Flywheel gear wrapping ANTs antsLongitudinalCorticalThickness.sh script.
This script creates a Single Subject Template from all the anatomical images and time
point based template.

## Usage

This gear should be run on the Subject level.

### Inputs

* __registered_predefined_atlases__ (file): Registered atlases to a population based
template.

``` text
<working_dir_name>
└── <template_folder_name>
    ├── Priors2
    │   ├── <nifti-file-name>
    │   ├── <nifti-file-name>
    │   ├── <nifti-file-name>
    │   ├── <nifti-file-name>
    │   ├── <nifti-file-name>
    │   └── <nifti-file-name>
    ├── brain_extraction_probability_mask
    │   └── <nifti-file-name>
    ├── brain_segmentation_template
    │   └── <nifti-file-name>
    ├── extraction_registration_mask
    │   └── <nifti-file-name>
    └── t1_registration_template
        └── <nifti-file-name>
```

As shown above, each directory should be labeled with one of the following names:

* Priors2
* brain_extraction_probability_mask
* brain_segmentation_template
* extraction_registration_mask
* t1_registration_template

Within each directory, it should contain only *ONE* template/mask image, except for the
`Priors2` directory.

*Note*: If registered predefined atlases template is not provided, the gear will use
the default atlases template which can be configured in the gear config (Default:
OASIS-30_Atropos_template).
*Note*: If registered predefined atlases template is not provided, the gear will use
the default atlases template which can be configured in the gear config (Default:
OASIS-30_Atropos_template).

### Configuration

* __debug__ (boolean, default: False): Include debug statements in output.
* __image_dimension__ (int, default: 3): 2 or 3 (for 2- or 3-dimensional image)
* __atropos_iteration__ (int, default: 5): Number of iterations within Atropos.
* __denoise_anatomical_image__ (int, default: 1): Denoise anatomical images.
* __number_of_modalities__ (int, default: 1): Number of modalities used to construct
the template:  For example,if one wanted to use multiple modalities consisting of T1,
T2, and FA components, it will be 3 modalities.
* __rigid_template_update_component__ (int, default: 0): Update the single-subject
template with the full affine transform (default 0).If 1, the rigid component of the
affine transform will be used to update the template. Using the rigid component is
desireable to reduce bias, but variations in the origin or head position across time
points can cause the template head to drift out of the field of view.
* __rigid_alignment_to_SST__ (int, default: 0): If 1, register anatomical images to
the single-subject template before processing with antsCorticalThickness. This
potentially reduces bias caused by variable orientation and voxel spacing
* __input_regex__ (str, default: ".*nii\\.gz"): Regular expression that matches files
to be used as anatomical image inputs. (Default '.*nii\\.gz').
<https://en.wikipedia.org/wiki/Regular_expression>.
* __input_tags__ (str, default: ""): Tag(s) that matches files to be used as anatomical
image inputs. When multiple tags are specified, they must be comma separated (e.g.
anatomical,ANTsLongitudinal)
* __atlases_template__ (str, default: "OASIS-30_Atropos_template"): If predefined
atlases are not provided as an input, the gear will use this as the default predefined
atlas template.

## Contributing

For more information about how to get started contributing to this gear,
checkout [CONTRIBUTING.md](CONTRIBUTING.md).
