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| mri_aparc2aseg - diffuses an annotation file from a surface in the cortical ribbon | mri_aparc2aseg - Maps the cortical labels from the automatic cortical parcellation (aparc) to the automatic segmentation volume (aseg). The result can be used as the aseg would. |
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| Diffuses labels from the surface to the volume. | Maps the cortical labels from the automatic cortical parcellation (aparc) to the automatic segmentation volume (aseg). The result can be used as the aseg would. The algorithm is to find each aseg voxel labeled as cortex (3 and 42) and assign it the label of the closest cortical vertex. If the voxel is not in the ribbon (as defined by mri/lh.ribbon and rh.ribbon), then the voxel is marked as unknown (0). This can be turned off with --noribbon. The cortical parcellation is obtained from subject/label/hemi.aparc.annot which should be based on the curvature.buckner40.filled.desikan_killiany.gcs atlas. The aseg is obtained from subject/mri/aseg.mgz and should be based on the RB40_talairach_2005-07-20.gca atlas. If these atlases are used, then the segmentations can be viewed with tkmedit and the FreeSurferColorLUT.txt color table found in $FREESURFER_HOME. These are the default atlases used by recon-all. |
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| mri_aparc2aseg bert Computes the aparc+aseg.mgz volume for subject bert == Example 2 == command foo -i f -o out -f fvalue description = Bugs = None = See Also = ["othercommand1"], ["othercommand2"] = Links = FreeSurfer, FsFast = Methods Description = |
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| description description |
mri_aparc2aseg --s bert tkmedit bert orig.mgz -segmentation mri/aparc+aseg.mgz \ $FREESURFER_HOME/FreeSurferColorLUT.txt |
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= References = ["References/Lastname###"] |
Computes the aparc+aseg.mgz volume for subject bert. |
Index
Contents
Name
mri_aparc2aseg - Maps the cortical labels from the automatic cortical parcellation (aparc) to the automatic segmentation volume (aseg). The result can be used as the aseg would.
Synopsis
mri_aparc2aseg [ options ]
Arguments
Required Flagged Arguments
--s argSubject |
subject |
recon-ed subject in the SUBJECTS_DIR |
Optional Flagged Arguments
--o argOutput |
output file |
output the segmentation volume (relative to the current dir) |
--a2005 |
use aparc.a2005 instead of aparc |
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--ribbon |
use mri/hemi.ribbon.mgz as a mask for the cortex |
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--annot argName |
use specified label file instead of aparc |
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--version |
display version |
show version information and exit |
Outputs
volume1 |
segmentation volume |
Description
Maps the cortical labels from the automatic cortical parcellation (aparc) to the automatic segmentation volume (aseg). The result can be used as the aseg would. The algorithm is to find each aseg voxel labeled as cortex (3 and 42) and assign it the label of the closest cortical vertex. If the voxel is not in the ribbon (as defined by mri/lh.ribbon and rh.ribbon), then the voxel is marked as unknown (0). This can be turned off with --noribbon. The cortical parcellation is obtained from subject/label/hemi.aparc.annot which should be based on the curvature.buckner40.filled.desikan_killiany.gcs atlas. The aseg is obtained from subject/mri/aseg.mgz and should be based on the RB40_talairach_2005-07-20.gca atlas. If these atlases are used, then the segmentations can be viewed with tkmedit and the FreeSurferColorLUT.txt color table found in $FREESURFER_HOME. These are the default atlases used by recon-all.
Examples
Example 1
mri_aparc2aseg --s bert tkmedit bert orig.mgz -segmentation mri/aparc+aseg.mgz \ $FREESURFER_HOME/FreeSurferColorLUT.txt
Computes the aparc+aseg.mgz volume for subject bert.
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>
Author/s
Doug Greve