fs2dicom 0.1.0

Create DICOM Segmentation Image and Structured Report objects from FreeSurfer segmentations

# fs2dicom
`fs2dicom` is a tool to convert [FreeSurfer](https://surfer.nmr.mgh.harvard.edu/) outputs to DICOM.

Two subcommands are implemented: `create-seg` and `create-sr`, to produce [DICOM Segmentation Image objects](https://qiicr.gitbooks.io/dicom4qi/content/results/seg.html), and DICOM Structured Report objects, respectively. `aseg.stats` to `DICOM-SR` using [dcmqi](https://github.com/QIICR/dcmqi/).

Currently, only [`aseg.mgz`](http://surfer.nmr.mgh.harvard.edu/fswiki/SubcorticalSegmentation/) and `aseg.stats` are supported and documented. Future versions may support other FreeSurfer segmentations and parcellations (such as thickness and volumes of different cortical regions)

## Dependencies
[dcmqi](https://github.com/QIICR/dcmqi) and [FreeSurfer](https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall) are required. Alternatively, instead of installing these programs locally, [Docker](https://docs.docker.com/install/) can be used instead to run the necessary commands. Using Docker is the default.

Note: future updates should be able to remove the FreeSurfer dependency, and replace its functionality with python-based tools.

## Installation
Clone the repo, cd into it, and run:
```
pip install -e .
```
This will install all python requirements needed to run `fs2dicom` (listed in `requirements.txt`).

## Usage
### `fs2dicom` base options
```
Usage: fs2dicom [OPTIONS] COMMAND [ARGS]...

Create DICOM Segmentation Image and Structured Report objects from
FreeSurfer segmentations.

Currently requires either docker OR FreeSurfer and dcmqi installed locally

Docker is the default way to run FreeSurfer and dcmqi commands needed to
create DICOM SEG/SR

A FreeSurfer License key is required to run the docker image. This can be
downloaded from: https://surfer.nmr.mgh.harvard.edu/registration.html

FreeSurfer commands are used to resample the aseg to native space Future
versions may remove this dependency

Options:
--dcmqi_type [docker|local] Use docker or local installed version of
dcmqi (default: docker)
--dcmqi_docker_image TEXT Name of the dcmqi docker image (default:
qiicr/dcmqi:latest)
--freesurfer_type [docker|local]
Use docker or local installed version of
freesurfer (default: docker)
--freesurfer_docker_image TEXT Name of the FreeSurfer docker image.
Currently only supports
corticometrics/fs6-base (default:
corticometrics/fs6-base:latest)
--fs_license_key TEXT Path to FreeSurfer License key file.
(default: path set by environment variable
FS_LICENSE_KEY)
-h, --help Show this message and exit.

Commands:
create-seg Creates a DICOM Segementation Image object ...
create-sr Creates a DICOM Structured Report object...
```
### `create-seg` subcommand options
```
Usage: fs2dicom create-seg [OPTIONS] T1_DICOM_FILE ASEG_IMAGE_FILE
[ASEG_DICOM_SEG_OUTPUT]

Creates a DICOM Segementation Image object from the T1_DICOM_FILE (one of
the T1w DICOM files processed with FreeSurfer) and ASEG_IMAGE_FILE, and
outputs to the ASEG_DICOM_SEG_OUTPUT file name (default: ./aseg.dcm)

Options:
--seg_metadata PATH Path to the DICOM SEG metadata schema describing the
aseg (default: provided within package)
-h, --help Show this message and exit.
```
### `create-sr` subcommand options
```
Usage: fs2dicom create-sr [OPTIONS] T1_DICOM_FILE ASEG_STATS_FILE
[ASEG_DICOM_SR_OUTPUT]

Creates a DICOM Structured Report object ASEG_DICOM_SR_OUTPUT (default:
./aseg-sr.dcm) using the values from the ASEG_STATS_FILE created by
FreeSurfer. The T1_DICOM_FILE (one of the T1w DICOM files processed with
FreeSurfer) and aseg_dicom_seg_file (default: ./aseg.dcm, specified with
--aseg_dicom_seg_file) are needed to provide context for this DICOM SR.
sr_metadata_output is also created (default: ./fs-aseg-sr.json, specified
with --sr_metadata_output), containing the values used to create the DICOM
SR.

Options:
--aseg_dicom_seg_file PATH DICOM SEG of the aseg, for example created by
`fs2dicom create-seg` (default: ./aseg.dcm)
--sr_metadata_output PATH JSON file output containing the values used to
create the DICOM SR (default: ./fs-aseg-sr.json)
--seg_metadata PATH Path to the DICOM SEG metadata schema describing
the aseg (default: provided within package)
--sr_template PATH Path to DICOM SR template that is filled in with
aseg.stats values (default: provided within
package)
-h, --help Show this message and exit.

```

## Descriptions of steps implemented by `fs2dicom`
Preprocessing (not done by fs2dicom):
- Run Freesurfer's [`recon-all`](https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable) on your input DICOM(s) to generate `aseg.mgz` and `aseg.stats`.

### `aseg.mgz` to `DICOM-SEG`
1. Call [`mri_vol2vol`](https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2vol) from FreeSurfer to resample `aseg.mgz` from FreeSurfer space to the native space of the input T1 DICOM, and convert to nifti.
```
mri_vol2vol \
--mov /path/to/aseg.mgz \
--targ /path/to/t1/dicom/file \
--regheader \
--nearest \
--o aseg_native.nii.gz
```
2. Use [`itkimage2segimage`](https://qiicr.gitbooks.io/dcmqi-guide/user_guide/itkimage2segimage.html) from [dmcqi](https://github.com/QIICR/dcmqi) to convert `aseg.nii.gz` to DICOM-SEG using [`fs-aseg.json`](fs2dicom/templates/fs-aseg.json) in this repo.
```
itkimage2segimage \
--inputDICOMDirectory /path/to/t1/dicom/directory \
--inputMetadata /path/to/fs2dicom/fs2dicom/templates/fs-aseg.json \
--inputImageList aseg_native.nii.gz \
--outputDICOM aseg.dcm
--skip
```

[`fs-aseg.json`](fs2dicom/templates/fs-aseg.json) maps [FreeSurfer aseg labels](https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI/FreeSurferColorLUT) to [SNOMED](https://www.snomed.org/) codes and preserves the FreeSurfer's recommended color scheme.

`fs-aseg.json` has been kindly provided by [Emily Lindemer](https://www.linkedin.com/in/emily-lindemer-87206667/)

See the [DCMQI gitbook](https://qiicr.gitbooks.io/dicom4qi/results/seg/freesurfer.html) for details

### `aseg.stats` to `DICOM-SR`
1. Read the `aseg.stats` file into a `pandas` dataframe
2. Fill in the [`fs-aseg-sr-template.json`](fs2dicom/templates/fs-aseg-sr-template.json) `jinja2` template with:
- the T1 DICOM file list,
- the name of the aseg `DICOM SEG` file, and
- the volume values from the `aseg.stats` dataframe
3. Create the `DICOM SR` file using `dcmqi`'s `tid1500writer`:
```
tid1500writer \
--inputImageLibraryDirectory /path/to/t1/dicom/directory \
--inputCompositeContextDirectory /path/to/aseg_dicom_seg/directory \
--outputDICOM aseg-sr.dcm \
--inputMetadata fs-aseg-sr.json # created in previous step
```
More information can be found here:
- [`tid1500writer` user guide](https://qiicr.gitbooks.io/dcmqi-guide/user_guide/tid1500writer.html)
- [example `--inputMetadata` json file](https://github.com/QIICR/dcmqi/blob/master/doc/examples/sr-tid1500-ct-liver-example.json)
- [aseg-specific example `--inputMetadata` json file](examples/fs-aseg-sr.json)
- Subject-specific modifications
- `"compositeContext"` needs to point to DICOM-SEG object
- `"imageLibrary"` needs to point to list of source MPRAGE dicoms
- `"Measurements"->"measurementItems"-"value"` needs to be harvested from `aseg.stats`
- `"Measurements"->"SourceSeriesForImageSegmentation"` needs to be set to the DICOM "Series Instance UID Attribute" (0020,000E)