bids_fastsurfer

Tool to create appropriate docker command to run fastsurfer from a BIDS dataset. Also ensure resolution is not too small for fastsurfer memory requirement. If too small (<0.5mm), resample the data first (see Warning below).

This is a BIDS app, so it complies with the command line call structure: bids_fastsurfer bids_dir derivatives_dir participant. See Usage below for details.

Usage

Example: singularity, full pipeline

git clone git@github.com:ln2t/bids_fastsurfer.git
cd bids_fastsurfer
source venv/bin/activate
pip install -r requirements.txt
python bids_fastsurfer.py /path/to/BIDS/dataset /path/to/output/folder/bids_fastsurfer participant --participant_label 42 --singularity

This will output a bash command to call singularity. Ensure the path to the singularity image is correct. A part from that, is it ready to run.

Example: singularity, segmentation only

git clone git@github.com:ln2t/bids_fastsurfer.git
cd bids_fastsurfer
source venv/bin/activate
pip install -r requirements.txt
python bids_fastsurfer.py /path/to/BIDS/dataset /path/to/output/folder/bids_fastsurfer participant --participant_label 42 --singularity --seg_only

This will output a bash command to call singularity. Ensure the path to the singularity image is correct. A part from that, is it ready to run.

Example: docker, full pipeline

git clone git@github.com:ln2t/bids_fastsurfer.git
cd bids_fastsurfer
source venv/bin/activate
pip install -r requirements.txt
python bids_fastsurfer.py /path/to/BIDS/dataset /path/to/output/folder/bids_fastsurfer participant --participant_label 42 --docker

This will output a bash command calling docker, with all paths and arguments already nice and ready to run.

Example: docker, segmentation only

git clone git@github.com:ln2t/bids_fastsurfer.git
cd bids_fastsurfer
source venv/bin/activate
pip install -r requirements.txt
python bids_fastsurfer.py /path/to/BIDS/dataset /path/to/output/folder/bids_fastsurfer participant --participant_label 42 --docker --seg_only

This will output a bash command calling docker, with all paths and arguments already nice and ready to run.

WARNING

FastSurfer for images of very high spatial resolution (<0.5mm) might crash due to GPU-memory issues. To circumvent this, bids_fastsurfer checks that the resolution in each direction is larger than 0.5mm. If not, it will downsample the data, which irremediably destroy information. Make sure you understand what this mean before using this tool. The downsampled data are stored in derivatives_dir/sourcedata and have the _resampled suffix.