how are you defining your ROI? Below is some info Im putting together on
segmentations, parcellations, and labels. It's still pretty raw, but it
might be useful to you.
Segmentation
- each voxel has an index
- index into lookup table (LUT), eg FreeSurferColorLUT.txt
- only one index per voxel
- surface or volume
- binary segmentation (mask) - 0 and 1
Parcellation/Annotation
- surface only ("surface annotation" is redundant)
- each vertex has a name
- inconvenient
- cross-reference to FreeSurferColorLUT.txt
Label
- a single segmentation/parcellation
- surface or volume
- text file with a list of 5 numbers for each vertex/voxel
- 1. VertexNo (0-based, ignored for volume labels)
2. X coordinate of voxel/vertex in tkreg space
3. Y coordinate of voxel/vertex in tkreg space
4. Z coordinate of voxel/vertex in tkreg space
5. Statistic (not used by all programs)
Color Table:
- List of segmentations/parcellations
- Each row has 6 columns:
1. Index
2. Name (no spaces)
3. Red (0-255)
4. Green (0-255)
5. Blue (0-255)
6. Statistic
Convert a set of labels into an annotation/parcellation:
mris_label2annot
Convert an annotation/parcellation to a set of surface labels:
mri_annotation2label
Convert an annotation/parcellation to a surface segmentation:
mri_annotation2label (name misleading)
Convert a single ROI in a volume or surface segmentation into a volume
or surface label:
mri_cor2label (surface or volume labels, name misleading)
Convert a set of volume labels into a volume segmentation:
mri_label2vol
Convert a set of surface labels to a surface segmentation:
No single program. Use mri_label2annot, then mri_annotation2label
Convert a label on one subject to a label on another subject:
mri_label2label (surface or volume labels)
Convert a surface segmentation to an annotation:
mris_seg2annot
Merge two or more labels together:
mri_mergelabels
Create a label from a bounding box:
bblabel
Merge an annotation/parcellation with a volume segmentation to create
a new volume segmentation: mri_aparc2aseg
Create a binary segmentation (mask) from a segmentation:
mri_binarize (use --match)
Create surface labels from thresholded surface activation maps:
mri_surfcluster
Create an annotation/parcellation from thresholded surface activation maps:
mri_surfcluster
Create a surface segmentation from thresholded surface activation maps:
mri_surfcluster
Create volume labels from thresholded volume activation maps:
mri_volcluster
Create a volume segmentation of activation clusters:
mri_volcluster
Gabriel GLZ wrote:
hello
in the case that i have a ROI and i don't know wich voxeles are in
there, or the coordenates of those voxeles, i want to create a
specific label that only contains those voxeles, how can i do that??'
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