FastSurfer Implementation #537

MatthieuJoulot · 2021-12-22T09:03:47Z

MatthieuJoulot
Dec 22, 2021
Collaborator

FastSurfer is a full FreeSurfer alternative. However, the processing is much faster: it takes 2 hours to process a subject, whereas FreeSurfer takes 10 to 15 hours. Therefore, we went into details to see if we could implement FastSurfer in Clinica.

Clinica version: 0.5.2

1. Dependencies

In that aspect, FastSurfer is compatible with Clinica, even though it is a little restrictive for a few dependancies.

2. Command

$FASTSURFER_HOME/run_fastsurfer.sh t1 --> your subject nii.gz
--sd --> your output
--sid --> your subject id
--batch --> number of batch (8 by default)
--surfreg --> run surface registration with FreeSurfer
--vol_segstats --> Additionally return volume-based apac.DKatlas+aseg statistics for DL based segmentation
--fsaparc --> Additionally return FS aparc segmentations and ribbon.

3. Outputs

The outputs generated are separated in two directories, one called “fsaverage” and the other one called by the name specified in the command, which is not the same as FreeSurfer in which there is only one directory. Inside, the outputs are structured the same way they are in FreeSurfer.

3.1. Output compatibility

3.1.1. Dwi-connectome

FastSurfer’s output are compatible with the dwi connectome pipeline.

3.1.2. Pet-Surface

FastSurfer’s ouput are compatible with the Pet-Surface pipeline.

3.1.3. Statistics

The inputs for this pipeline are not generated by FastSurfer. It may be possible to generate them using the generated outputs and the command mris_preproc from FreeSurfer.

3.1.4. T1 FreeSurfer Longitudinal

The outputs of FastSurfer seem to be compatible with the FreeSurfer longitudinal pipeline. However, since the FreeSurfer documentation is not clear on the inputs used, it is hard to tell. It worked when tested, but it should be double checked if the implementation is considered again at some point.

3.2. Outputs values

Even though FastSurfer is supposed to be a full alternative to FreeSurfer, it should be noted that the results will be slightly different. This is detailed in the FastSurfer article.