well... my ROI is from another program (tha's why, i'm taking it as a different, not sinonimous), wich determines some parameters that i'm looking for... but that zones do not correspond or match with the parcellations of FS, so i need to know the location for the voxels, and how to make a label takin' those parameters on FS

 





Date: Mon, 22 Dec 2008 14:35:19 -0500
From: greve@nmr.mgh.harvard.edu
To: gabriellbk@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] (no subject)

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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