master branch
brainlife.io version of multi atlas transfer tools (maTT). This app takes in a completed recon-all
FreeSurfer directory, and outputs a volumetric parcellation in the indiviual's T1w space. These tools warp the parcellations to the subject space using the warp information provided by FreeSurfer. This is an implemenation of maTT2, which uses the gcs files trained on the mindboggle-101 data. The GCS files are automatically pulled from the maTT fishare directory if not present locally.
Check out the maTT github repo for more info and the latest version of maTT.
brainlife.io is publicly funded and for the sustainability of the project it is helpful to Acknowledge the use of the platform. We kindly ask that you acknowledge the funding below in your publications and code reusing this code.
We we think you should cite the following when code using this code.
You can submit this App online at http://doi.org/10.25663/bl.app.23 via the "Execute" tab.
config.json
with something like the following content with paths to your input files.{
"fsin": "./path/to/freesurferdir/",
"atlas": "atlasname"
}
Note: the atlasname should be the name of one of the available atlases provided in the figsshare repo.
main
./main
All output files will be generated under the current working directory (pwd), in directories called parc-vol
, parc-surf
, and mask
.
Inside parc-vol
there will be:
parc.nii.gz
key.txt
label.json
Inside parc-surf
there will be:
?h.parc.inflated.gii
?h.parc.pial.gii
?h.parc.white.gii
?h.parc.annot.gii
key.txt
label.json
Also, there is a volumetric mask in the mask
directory.
This App uses singularity to run. If you don't have singularity, you can run this script in a unix enviroment with:
This material is based upon work supported by the National Science Foundation Graduate Research Fellowship under Grant No. 1342962. Any opinion, findings, and conclusions or recommendations expressed in this material are those of the authors(s) and do not necessarily reflect the views of the National Science Foundation.