Index TableOfContents

Name

mri_ca_train - create a GCA from MNI and xfm files

Synopsis

mri_ca_train [options] <subject 1> <subject 2> ... <output gca fname>

Arguments

Positional Arguments

<subject 1>

subject 1

<subject 2>

subject 2

<output file>

output file

Required Flagged Arguments

-parc_dir

segmentation directory (path relative to $subject/mri

Optional Flagged Arguments

-spacing

spacing of classifiers in canonical space

-gradient

use intensity gradient as input to classifier

-mask volname

use volname as a mask

-node_spacing

spacing of classifiers in canonical space i.e. memory you devote to intensity distribution

-prior_spacing

spacing of class priors in canonical space i.e. memory you devote to prior probabity distributions

-input name

specifying training data (path relative to $subject/mri). can specify multiple inputs. If not specified, "orig" is used. Using orig is sufficient for an atlas created with MPRAGES, but for other data types (i.e. multi-echo flash) this volume should be choosen more carefully, see example 2.

-T1

input volume (i.e. nu, norm.mgh etc)

-flash

specifies the atlas as either single-echo or multi-echo

-xform

reference transform

Outputs

<output file>

gca file - gaussian class array file, in this instance essentially a probabilistic map

Description

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Examples

Example 1

mri_ca_train -prior_spacing 2 -node_spacing 8 -mask brain -parc_dir esegatlast -xform manual_registration.xfm -T1 nu subject1 single_one.gca

Example 2

mri_ca_train -node_spacing 4 -prior_spacing 2 -parc_dir esegatlast -xform talairach_one.m3d -input flash30_avg.mgz -input flash5_avg.mgz $SUBJECTS multi_one.gca

Bugs

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See Also

["mri_em_register"], ["mri_ca_normalize"]

Links

FreeSurfer

Methods Description

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References

["References/Lastname###"]

Reporting Bugs

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

Author/s

BruceFischl