SVREG: Output

In the following, fileprefix is the MRI file’s prefix (e.g. “brainsuite_subj1_m6” for the file “brainsuite_subj1_m6.nii.gz”) and hemi is “left” or “right”, for the left or right hemispheres respectively.

Surface Files
Filename Description
fileprefix.hemi.inner.cortex.svreg.dfs Labeled inner cortical surface of the subject
fileprefix.hemi.mid.cortex.svreg.dfs Labeled mid cortical surface of the subject. Vertex-wise cortical thickness measurements are stored in the “attributes” field
fileprefix.hemi.pial.cortex.svreg.dfs Labeled pial cortical surface of the subject
atlas.hemi.mid.cortex.svreg.dfs Labeled mid cortical surface of the target.
Curves Files
Filename Description
fileprefix.hemi.mapped.dfc Transferred curves from the atlas to the subject
fileprefix.hemi.mapped.all.dfc A larger set of transferred curves from the atlas to the subject
fileprefix.hemi.mapped.refined.dfc Transferred and refined curves from the atlas to the subject
Volume Files
Filename Description
fileprefix.svreg.nii.gz Warped atlas volume
fileprefix.inv.svreg.map.nii.gz Inverse of the 3D map from subject to atlas. This map is from atlas to subject
fileprefix.svreg.map.nii.gz 3D map from subject to atlas volume
fileprefix.svreg.label.nii.gz Warped labels of the atlas volume
Information Files
Filename Description
fileprefix.svreg.version text file showing version of svreg that was used.
fileprefix.roiwise.stats.txt Tab-deliminated text file containing the volume (mm3) and (where applicable) average cortical thickness (mm) of labeled structures.
Some important files in fileprefix.svreg.tmp directory*
Filename Description
fileprefix.svreg.nii.gz atlas volume mapped to subject using svreg map.
fileprefix.invsvreg.nii.gz subject mapped to atlas using inverse of svreg map.
fileprefix.svreg.jacobian.nii.gz Jacobian determinant of the svreg map.

* In addition to these files, there are several more files in the temp directory that are useful for debugging purposes.

Outputs of thicknessPVC script (Separate from SVReg)
Filename Description
fileprefix.GM_frac.nii.gz Gray matter tissue fraction for each voxel.
fileprefix.heat_map_sol.nii.gz Solution of heat equation.
fileprefix.pvc-thickness_0-6mm.isosurface.dfs Mid cortex defined by heat equation .attributes field in this file contains the computed thickness values.
fileprefix.pvc-thickness_0-6mm.mid.cortex.dfs The thickness values computed on to the mid cortex (thickness stored in .attributes field).
fileprefix.heat_sol_comp.mat Solution of heat equation that can be loaded in MATLAB.
fileprefix.pvc-thickness_0-6mm.left.mid.cortex.dfs Thickness values for the left mid cortex (thickness stored in .attributes field).
fileprefix.pvc-thickness_0-6mm.right.mid.cortex.dfs Thickness values for the right mid cortex (thickness stored in .attributes field).
atlas.pvc-thickness_0-6mm.left.mid.cortex.dfs Thickness values for the left mid cortex, mapped to atlas (thickness stored in .attributes field).
atlas.pvc-thickness_0-6mm.right.mid.cortex.dfs Thickness values for the right mid cortex, mapped to atlas (thickness stored in .attributes field).