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Also, run mri_label2vol --help for more information
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  --temp f_000.bshort   --temp f.nii.gz
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  --o cent-lh_000.bshort   --o cent-lh.nii.gz
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  -overlay ./cent-lh_000.bshort   -overlay ./cent-lh.nii.gz
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  --temp f_000.bshort   --temp f.nii.gz
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  --o cent-lh_000.bshort   --o cent-lh.nii.gz

Index

Name

mri_label2vol - creates mgz volume from a label or set of labels

Synopsis

mri_label2vol [--flag argument] Also, run mri_label2vol --help for more information

Arguments

Positional Arguments

none

Required Flagged Arguments

--label, --annot, or --seg are not to be used together.

--label labelfile

Label file

For multiple labels, use multiple --label flags.

--annot annotfile

Annotation file

--seg segpath

Path to segmentation

--temp tempvolid

Template volume

The output volume will have the same size and geometry as the template.

Optional Flagged Arguments

-flag3 arg3

brief description

detailed description (eg, help file information)

-flag4 arg4

brief description

detailed description (eg, help file information)

Outputs

--o volid

Single frame output volume (any mri_convert format accepted)

volume2

description

Description

Converts a label or a set of labels into a volume. For a single label, the volume will be binary: 1 where the label is and 0 where it is not. For multiple labels, the volume will be 0 where no labels were found otherwise the value will the the label number. For a voxel to be declared part of a label, it must have enough hits in the voxel and it must have more hits than any other label.

Examples

Example 1

Convert a label into a binary mask in the functional space; require that a functional voxel be filled at least 50% by the label:

mri_label2vol 
  --label lh-avg_central_sulcus.label 
  --temp f.nii.gz 
  --reg register.dat 
  --fillthresh .5 
  --o cent-lh.nii.gz

To see how well the label is mapped into the functional volume, run

tkmedit bert orig 
  -overlay ./cent-lh.nii.gz 
  -overlay-reg ./register.dat -fthresh .5 -fmid 1

Then load the label with File->Label->LoadLabel. The label should overlap with the overlay. The overlap will not be perfect but it should be very close.

Example 2

mri_label2vol 
  --label lh-avg_central_sulcus.label 
  --temp f.nii.gz 
  --reg register.dat 
  --fillthresh .3 
  --proj frac 0 1 .1 
  --subject bert --hemi lh
  --o cent-lh.nii.gz

Convert a surface label into a binary mask in the functional space. Fill in all the cortical gray matter. Require that a functional voxel be filled at least 30% by the label:

Bugs

When the output type is COR, all the voxels will be zero. The work-around is to save it as some other type, then use mri_convert with -no_rescale 1 to convert it to COR.

Cannot convert surface labels with different hemispheres.

See Also

mri_label2label, mri_cor2label, mri_annotation2label, mri_mergelabels, tkregister2, mri_convert, tkmedit, tksurfer

Links

FreeSurfer, FsFast

Methods Description

description
description

References

References/Lastname###

Reporting Bugs

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

Author/s

JaneSmith

mri_label2vol (last edited 2017-11-30 11:34:02 by MorganFogarty)