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'''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 ==

== Optional Flagged Arguments ==
|| -o <output volume>  || write aseg including CC to ../mri/<output volume> ||
|| -aseg <aseg volume> || read aseg from ../mrii/<aseg volume> ||
|| -sdir <directory path> || set SUBJECTS_DIR to <directory path> ||
|| -lta <fname> || write rotation lta to global <fname> ||
|| -f || include fornix in segmentation ||
|| -force || process regardless of existing CC in input. ||
|| -d <int> || subdivide into <int> segments ||
|| -t <int> || setting CC thickness to <int> mm, distance in mm to extend CC off the midline. ||
|| -s <int> || skipping <int> voxels in rotational align ||
|| -m <float> || set max of rotations to be searched (default=7deg) ||

= 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 =
FreeSurfer, FsFast

= Methods Description =
{{{
description
description
}}}

= References =
[[References/Lastname###]]

= Reporting Bugs =
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>

= Author/s =
AllisonStevens