Index TableOfContents

Name

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

Synopsis

mri_label2vol [--flag argument]

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

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

tkmedit bert orig

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

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