Index TableOfContents
Name
mri_cc - segments the corpus callosum into five separate labels in the subcortical segmentation volume 'aseg.mgz'
Synopsis
mri_cc [<options>] <subject name>
Arguments
Positional Arguments
argA |
brief description |
detailed description (eg, help file information) |
argB |
brief description |
detailed description (eg, help file information) |
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
-flag3 arg3 |
brief description |
detailed description (eg, help file information) |
-flag4 arg4 |
brief description |
detailed description (eg, help file information) |
Outputs
volume1 |
description |
volume2 |
description |
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
command foo -i f -o out
description
Example 2
command foo -i f -o out -f fvalue
description
Bugs
None
See Also
["othercommand1"], ["othercommand2"]
Links
Methods Description
description description
References
["References/Lastname###"]
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>