Index TableOfContents
Name
mri_cc - segments the corpus callosum into five separate labels in the subcortical segmentation volume 'aseg.mgz'
Synopsis
mri_cc <invol> <outvol> <subject name>
Arguments
Positional Arguments
|| invol || input volume || outvol || output volume ||
Required Flagged Arguments
-flag1 arg1 |
brief description |
detailed description (eg, help file information) |
-flag2 arg2 |
brief description |
detailed description (eg, help file information) |
Optional Flagged Arguments
-o <output volume> |
output file |
-aseg <aseg volume> |
show automatic segmentation (must already exist) |
Outputs
outvol |
output volume |
Description
The divisions of the cc are equally spaced in terms of distance along the primary eigendirection (pretty much the long axis) of the cc.
The lateral extent can be changed with the -T <thickness> parameter, where <thickness> is the distance off the midline (so -T 1 would result in the who CC being 3mm thick). The default is 2 so it's 5mm thick. The aseg.stats values should be volume.
To make the subdivisions stand-out, you would need to modify the FreeSurferColorLUT.txt. This will work:
251 |
CC_Posterior |
255 |
0 |
64 |
0 |
252 |
CC_Mid_Posterior |
0 |
0 |
112 |
0 |
253 |
CC_Central |
255 |
0 |
160 |
0 |
254 |
CC_Mid_Anterior |
0 |
0 |
208 |
0 |
255 |
CC_Anterior |
255 |
0 |
255 |
0 |
The 3 values after the name are the RGB that the label is displayed in.
Here, the red value of each alternate subdivision is turned to full intensity, which makes the division easy to see in tkmedit:
tkmedit <subjid> orig.mgz -segmentation aseg.mgz
Examples
Example 1
mri_cc -aseg aseg.mgz -o aseg.auto_CCseg.mgz bert
Uses the aseg volume and creates aseg.auto_CCseg.mgz with five divisions of the corpus callosum.
Bugs
None
See Also
["mri_ca_label"]
Links
Methods Description
description description
References
["References/Lastname###"]
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>