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: greve@nmr.mgh.harvard.eduTo: gabriellbk@hotmail.comCC: freesurfer@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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