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 -0500From: gr...@nmr.mgh.harvard.eduto:
gabriel...@hotmail.comcc: freesur...@nmr.mgh.harvard.edusubject: 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
1Parcellation/Annotation - surface only ("surface annotation" is redundant) -
each vertex has a name - inconvenient - cross-reference to
FreeSurferColorLUT.txtLabel - 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_label2annotConvert an annotation/parcellation
to a set of surface labels:mri_annotation2labelConvert an
annotation/parcellation to a surface segmentation:mri_annotation2label (name
misleading)Convert a single ROI in a volume or surface segmentation into a
volumeor surface label:mri_cor2label (surface or volume labels, name
misleading)Convert a set of volume labels into a volume
segmentation:mri_label2volConvert a set of surface labels to a surface
segmentation:No single program. Use mri_label2annot, then
mri_annotation2labelConvert 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_seg2annotMerge two or more labels
together:mri_mergelabelsCreate a label from a bounding box:bblabelMerge an
annotation/parcellation with a volume segmentation to createa new volume
segmentation: mri_aparc2asegCreate a binary segmentation (mask) from a
segmentation:mri_binarize (use --match)Create surface labels from thresholded
surface activation maps:mri_surfclusterCreate an annotation/parcellation from
thresholded surface activation maps:mri_surfclusterCreate a surface
segmentation from thresholded surface activation maps:mri_surfclusterCreate
volume labels from thresholded volume activation maps:mri_volclusterCreate a
volume segmentation of activation clusters:mri_volclusterGabriel 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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gr...@nmr.mgh.harvard.edu
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