Name

mri_ca_normalize - creates a normalized volume using the brain volume and an input gca file

Synopsis

mri_ca_normalize [<options>] <inbrain1> <inbrain2> ... <atlas> <transform file> <output1> <output2> ...

Arguments

Positional Arguments

inbrain1	input volume
inbrain2	input volume
atlas	atlas file in gca format
xform	tranform file in lta format
output1	output volume
output2	output volume

Required Flagged Arguments

None

Optional Flagged Arguments

-mask	specifies volume to use as mask
-p	specifies the percentage of likely wm to use as control points, the default setting is 50%

Outputs

outvol

output volume in either mgh or mgz format

Description

description

Examples

Example 1

mri_ca_normalize -mask -p 0.25 subject1/mri/brain subject1/mri/nu single_one.gca subject1/mri/transforms/talairach_one.lta subject1/mri/norm_one.mgh

Bugs

None

Links

FreeSurfer, FsFast

Methods Description

??

References

["References/Lastname###"]

Reporting Bugs

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

Author/s

BruceFischl

-  ⇤ ← Revision 1 as of 2004-08-23 15:27:24 → 
  Size: 1165
  Editor: MichaelOgrydziak
  Comment:
+   ← Revision 3 as of 2005-08-17 15:58:34 → ⇥
  Size: 1647
  Editor: ElizabethFenstermacher
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
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+[[Navigation(children)]]
'''Index'''
[[TableOfContents]]
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+Line 14:
-mri_ca_normalize - ?
+mri_ca_normalize - creates a normalized volume using the brain volume and an input gca file
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+Line 17:
-mri_ca_normalize [in brain] [atlas] [transform file] [output file name]
+ mri_ca_normalize [<options>] <inbrain1> <inbrain2> ... <atlas> <transform file> <output1> <output2> ...
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+Line 19:
-= Positional Arguments =
|| [in brain] || ? ||
|| [atlas] || ? ||
|| [transform file] || ? ||
|| [output file name] || ? ||
+= Arguments =
== Positional Arguments ==
||inbrain1 || input volume||
||inbrain2 || input volume||
||atlas ||atlas file in gca format||
||xform  || tranform file in lta format||
||output1 || output volume||
||output2 || output volume||
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+Line 28:
-= Required Flagged Arguments =
none
+== Required Flagged Arguments ==
None
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+Line 31:
-= Optional Flagged Arguments =
none
+== Optional Flagged Arguments ==
||-mask || specifies volume to use as mask ||
||-p || specifies the percentage of likely wm to use as control points, the default setting is 50%  ||
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+Line 36:
-|| output file name || ? ||
+|| outvol || output volume in either mgh or mgz format ||
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+Line 43:
-command foo -i f -o out
+mri_ca_normalize -mask -p 0.25 subject1/mri/brain subject1/mri/nu single_one.gca subject1/mri/transforms/talairach_one.lta subject1/mri/norm_one.mgh
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+Line 45:
-description

== Example 2 ==
command foo -i f -o out -f fvalue

description
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-description
description
+??
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-JaneSmith
+BruceFischl