SynthStrip

https://surfer.nmr.mgh.harvard.edu/docs/
Admin
SynthStrip is a skull-stripping tool that extracts brain voxels from various brain imaging...
Tokens:1,774
Snippets:24
Trust Score:10
Update:5 months ago
Show doc for...
Tokens:
Raw
### Download SynthStrip Docker Wrapper Script

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

Download the Docker wrapper script for running SynthStrip and make it executable.

```bash
curl -O https://raw.githubusercontent.com/freesurfer/freesurfer/dev/mri_synthstrip/synthstrip-docker && chmod +x synthstrip-docker
```

--------------------------------

### Download SynthStrip Singularity Wrapper Script

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

Download the Apptainer (Singularity) wrapper script for running SynthStrip and make it executable.

```bash
curl -O https://raw.githubusercontent.com/freesurfer/freesurfer/dev/mri_synthstrip/synthstrip-singularity && chmod +x synthstrip-singularity
```

--------------------------------

### Visualize Label Maps with Freeview

Source: https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/data/README

This command demonstrates how to use Freeview to visualize image and label map files, specifying a custom LUT file for label interpretation. Ensure you are in the correct directory containing the image and label files.

```bash
cd ixi_t1_002
freeview image.nii.gz labels.nii.gz:colormap=lut:lut=../seg_labels.txt
```

--------------------------------

### Download and Verify SynthStrip Dataset

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

Download the SynthStrip dataset and its checksums using curl, then verify the integrity and extract the archives using shasum and tar.

```bash
curl -O https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/data/SHA256
curl -O https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/data/synthstrip_data_v1.5.tar
curl -O https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/data/synthstrip_data_v1.5_2d.tar
shasum -c SHA256
tar -xf synthstrip_data_v1.5.tar
tar -xf synthstrip_data_v1.5_2d.tar
```

--------------------------------

### Basic SynthStrip Skull-Stripping

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

Perform basic skull-stripping on an input image and save the output to a specified file. Replace 'mri_synthstrip' with the appropriate wrapper script for containerized execution.

```bash
mri_synthstrip -i input.nii.gz -o stripped.nii.gz
```

--------------------------------

### SynthStrip Skull-Stripping Excluding CSF

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

Perform skull-stripping while excluding surrounding Cerebrospinal Fluid (CSF) and controlling the boundary distance. Use the `--no-csf` flag to exclude CSF and the `-b` option to adjust the boundary distance.

```bash
mri_synthstrip -i input.nii -o stripped.nii --no-csf
```

--------------------------------

### SynthStrip Skull-Stripping with Binary Mask Output

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

Skull-strip an input image and save both the stripped image and a binary brain mask to separate files. This command is applicable to both FreeSurfer and containerized versions.

```bash
mri_synthstrip -i input.mgz -o stripped.mgz -m mask.mgz
```
Tokens:
Raw