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.
| 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. |
| 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 |
| 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 |
| 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. |
| 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.
| 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). |
