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NeuroDesk / neurocontainers

The containers can be used in combination with our transparent singularity or neurocommand tool, that wrap the executables inside a container to make them easily available for pipelines
https://www.neurodesk.org
MIT License
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add synthstrip #155

Open stebo85 opened 2 years ago

stebo85 commented 2 years ago

https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/

but it's also included in the new fressurfer release

Vbitz commented 3 weeks ago

Already included in NeuroDesk with freesurfer/7.4.1 .

(base) jovyan@neurodesktop-2024-05-25:~$ ml load freesurfer/7.4.1
(base) jovyan@neurodesktop-2024-05-25:~$ mri_synthstrip 
Robust, universal skull-stripping for brain images of any type.
usage: mri_synthstrip [-h] -i file [-o file] [-m file] [-g] [-b BORDER] [--no-csf]
                      [--model file]

optional arguments:
  -h, --help            show this help message and exit
  -i file, --image file
                        Input image to skullstrip.
  -o file, --out file   Save stripped image to path.
  -m file, --mask file  Save binary brain mask to path.
  -g, --gpu             Use the GPU.
  -b BORDER, --border BORDER
                        Mask border threshold in mm. Default is 1.
  --no-csf              Exclude CSF from brain border.
  --model file          Alternative model weights.

If you use SynthStrip in your analysis, please cite:
----------------------------------------------------
SynthStrip: Skull-Stripping for Any Brain Image
A Hoopes, JS Mora, AV Dalca, B Fischl, M Hoffmann
NeuroImage 206 (2022), 119474
https://doi.org/10.1016/j.neuroimage.2022.119474 

Website: https://w3id.org/synthstrip
stebo85 commented 3 weeks ago

yes, but we need it as a separate container to include as baseline for other containers.