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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