Differences between revisions 1 and 7 (spanning 6 versions)

Index

Contents

Name
Synopsis
Arguments
Outputs
Description
Examples
Bugs
See Also
Links
Methods Description
References
Reporting Bugs
Author/s

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 be 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.

Example 3

mri_label2vol 
  --label lh-avg_central_sulcus.label 
  --temp f.nii 
  --reg register.dat 
  --proj abs -3 -2 .1 
  --subject bert --hemi lh
  --o cent-lh.nii

Convert a surface label into a binary mask in the functional space. Sample a 1mm ribbon 2mm below the gray/white surface. Do not require a fill threshold.

Example 4

mri_label2vol 
  --label lh-avg_central_sulcus.label 
  --label lh-avg_calcarine_sulcus.label 
  --temp $SUBJECTS_DIR/bert/orig
  --identity
  --o cent_calc.img

Convert two labels into a volume in the same space as the labels. The voxels corresponding to lh-avg_central_sulcus.label will have a of value of 1 whereas those assigned to lh-avg_calcarine_sulcus.label will have a value of 2.

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.

Links

FreeSurfer, FsFast

Methods Description

description
description

References

References/Lastname###

Reporting Bugs

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

Author/s

JaneSmith

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-otherwise the value will the the label number. For a voxel to be
+otherwise the value will be the label number. For a voxel to be
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+{{{
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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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+{{{
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-  -overlay ./cent-lh_000.bshort
+  -overlay ./cent-lh.nii.gz
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+}}}
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+{{{
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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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-be filled at least 30% by the label:
+be filled at least 30% by the label.

== Example 3 ==
{{{
mri_label2vol 
  --label lh-avg_central_sulcus.label 
  --temp f.nii 
  --reg register.dat 
  --proj abs -3 -2 .1 
  --subject bert --hemi lh
  --o cent-lh.nii
}}}
Convert a surface label into a binary mask in the functional space.
Sample a 1mm ribbon 2mm below the gray/white surface. Do not require a 
fill threshold.

== Example 4 ==
{{{
mri_label2vol 
  --label lh-avg_central_sulcus.label 
  --label lh-avg_calcarine_sulcus.label 
  --temp $SUBJECTS_DIR/bert/orig
  --identity
  --o cent_calc.img
}}}
Convert two labels into a volume in the same space as the labels. The voxels corresponding to lh-avg_central_sulcus.label will have a of 
value of 1 whereas those assigned to lh-avg_calcarine_sulcus.label will have a value of 2.
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-["mri_label2label"], ["mri_cor2label"], ["mri_annotation2label"], ["mri_mergelabels"], ["tkregister2"], ["mri_convert"], ["tkmedit"], ["tksurfer"]
+[[mri_label2label]], [[mri_vol2label]], [[mri_annotation2label]], [[mri_mergelabels]], [[tkregister2]], [[mri_convert]], [[tkmedit]], [[tksurfer]]
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+Line 129:
-["References/Lastname###"]
+[[References/Lastname###]]