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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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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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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Hi,
we have structural data at two time points (t1/t2) for two different groups (intervention vs control). After processing the data using the long stream, we want to model the group X time interactions to detect intervention specific changes in cortical thickness over time.
Q1) How would you suggest modeling such an interaction?
Q2) Related to the first question, instead of two inputs (t1 and t2) per subject, would you recommend submitting one difference map (t2-t1) for each subject to the GLM, and do something like 1 -1 0? (interv_diff, cont_diff, age)
Thanks for your time, Lars
Hi Lars, I would use the 2nd one. See
https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis
Lars Tjelta Westlye wrote:
Hi,
we have structural data at two time points (t1/t2) for two different groups (intervention vs control). After processing the data using the long stream, we want to model the group X time interactions to detect intervention specific changes in cortical thickness over time.
Q1) How would you suggest modeling such an interaction?
Q2) Related to the first question, instead of two inputs (t1 and t2) per subject, would you recommend submitting one difference map (t2-t1) for each subject to the GLM, and do something like 1 -1 0? (interv_diff, cont_diff, age)
Thanks for your time, Lars
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freesurfer@nmr.mgh.harvard.edu
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Doug Greve -
Douglas N Greve
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Gabriel GLZ -
Lars Tjelta Westlye