Deletions are marked like this. | Additions are marked like this. |
Line 43: | Line 43: |
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 |
Index
Contents
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.
See Also
mri_label2label, mri_vol2label, mri_annotation2label, mri_mergelabels, tkregister2, mri_convert, tkmedit, tksurfer
Links
Methods Description
description description
References
Reporting Bugs
Report bugs to <analysis-bugs@nmr.mgh.harvard.edu>