SVReg: Usage

• fileprefix.bfc.nii.gz
• fileprefix.cerebrum.mask.nii.gz
• fileprefix.cortex.dewisp.mask.nii.gz
• fileprefix.inner.cortex.dfs
• fileprefix.left.inner.cortex.dfs
• fileprefix.left.pial.cortex.dfs
• fileprefix.mask.nii.gz
• fileprefix.pial.cortex.dfs
• fileprefix.pvc.frac.nii.gz
• fileprefix.right.inner.cortex.dfs
• fileprefix.right.pial.cortex.dfs
• fileprefix.warp

If you do not already have these files, they can be generated by running the BrainSuite scripts or by using the graphical interface and running the complete Cortical Surface Extraction Sequence with the “save output of each stage automatically” box checked.

1. Make sure your original MRI file <e.g. “subj1.nii.gz”> and related required files (see above) are placed in the same directory. It is recommended that you place these files in a separate directory as SVReg generates a lot of files.
2. Open your original MRI file from this directory.
3. Open the Surface/Volume Registration dialog box by clicking Cortex→Surface/Volume Registration
4. (Optional) Select the Labeled Atlas using the drop-down menu. Select the appropriate options.
5. Click “Apply” to run through all stages of registration and labeling automatically, or “Step >” to step through them individually. 
6. Inspect the labeled surfaces and volumes in BrainSuite.
7. SVReg will spawn windows detailing its progress and letting you know if something is wrong. Surface and volume registration is a computation-intensive procedure and you may notice some slowdown in other applications while this process is underway.

1. Make sure your original MRI file <e.g. “subj1.nii.gz”> and related required files (see above) are placed in the same directory. It is recommended that you place these files in a separate directory as SVReg generates a lot of files.
2. Add the SVReg directory to your system’s path, or navigate to where its binaries and scripts are located.
3. Run the SVReg script corresponding to your system. This will execute the surface and volume registration modules and generate the labeled surfaces and volumes within your working directory. Note that *_file_prefix is the path of the subject or atlas file followed by its filename without the file extension. Atlas folders can be found in the SVReg directory.

svreg.exe <subject_file_prefix> [<atlas_file_prefix>] [-<flags>]

Example: svreg.exe "C:\Users\username\testsubject\testsubject" -t

Note that atlas_file_prefix and flags are optional, as indicated by the square brackets; SVReg uses the included atlas and runs in verbose mode, cleaning up intermediate files, and without refinement by default.

svreg.sh <subject_file_prefix> [<atlas_file_prefix>] [-<flags>]

Example: svreg.sh ~/testsubject/testsubject /BrainSuite16a1/svreg/BrainSuiteAtlas1/mri -t

Note that atlas_file_prefix and flags are optional, as indicated by the square brackets; SVReg uses the included atlas and runs in verbose mode, cleaning up intermediate files, and without refinement by default.

SVReg versions 15a and above contains a new labeled atlas named BCI-DNI_atlas. The description of this new atlas can be found here.

Example Result