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mri_cc [<options>] <subject name> mri_cc <invol> <outvol>  <subject name>
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|| argA || brief description || detailed description (eg, help file information) ||
|| argB || brief description || detailed description (eg, help file information) ||
|| invol || input volume ||
|| outvol || output volume ||
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|| -flag3 arg3 || brief description ||detailed description (eg, help file information) ||
|| -flag4 arg4 || brief description ||detailed description (eg, help file information) ||
|| -o <output volume> || output file ||
|| -aseg <aseg volume> || show automatic segmentation (must already exist) ||
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|| volume1 || description ||
|| volume2 || description ||
|| outvol || output volume ||
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||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||
||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||
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command foo -i f -o out mri_cc -aseg aseg.mgz -o aseg.auto_CCseg.mgz bert
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description Uses the aseg volume and creates aseg.auto_CCseg.mgz with five divisions of the corpus callosum.
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== Example 2 ==
command foo -i f -o out -f fvalue

description
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["othercommand1"], ["othercommand2"] ["mri_ca_label"]
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JaneSmith AllisonStevens

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

FreeSurfer, FsFast

Methods Description

description
description

References

["References/Lastname###"]

Reporting Bugs

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

Author/s

AllisonStevens

mri_cc (last edited 2011-12-21 16:30:00 by LouisVinke)