Freesurfer Subparcellation - Revision history

Chris at 18:30, 27 September 2022

2022-09-27T18:30:24Z

← Older revision		Revision as of 14:30, 27 September 2022
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	Freesurfer annotations and labels describe swaths of cortical regions, defined anatomically during the recon-all process, or functionally or statistically (e.g., significant GLM clusters). Tools exist to further subdivide these regions to the desired level of granularity.		Freesurfer annotations and labels describe swaths of cortical regions, defined anatomically during the recon-all process, or functionally or statistically (e.g., significant GLM clusters). Tools exist to further subdivide these regions to the desired level of granularity.
			= Using AnchorBar =
			AnchorBar is a set of Python tools developed in our lab that maintain a database of a set of annotations and supports set operations on the labels associated with one or more annotations. For example, an atlas-based annotation can be intersected with a functional annotation (e.g., from a group-level GLM) to subdivide large functional clusters along anatomical boundaries.

	== Using mris_divide_parcellation ==		= Using mris_divide_parcellation =
	This program divides one or more parcellations into divisions		This program divides one or more parcellations into divisions
	perpendicular to the long axis of the label. The number of divisions		perpendicular to the long axis of the label. The number of divisions
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	divisions. The first division has the same name as the original label.		divisions. The first division has the same name as the original label.

	=== Sample Split File (Functional Clusters) ===		== Sample Split File (Functional Clusters) ==
	In this example, I have carried out a one-sample group mean (OSGM) analysis and did a cluster-size threshold. This saved a number of clusters in two .annot files (one in each hemisphere). There are also some ''*.cluster.summary'' files in this directory. Reading these files, I see the smallest clusters are about 120mm<sup>2</sup>. I would like to subdivide the larger clusters so that they are all between about 100-150mm<sup>2</sup>. I load the corresponding .annot file in Freesurfer just to verify the cluster names (the summary file lists 10 clusters, but the names do not follow a consistent naming convention). From the file, I see that clusters 1,2,3,4,6 and 8 need to be subdivided. Simple division by the desired cluster size tells me the number of divisions I want for each cluster:		In this example, I have carried out a one-sample group mean (OSGM) analysis and did a cluster-size threshold. This saved a number of clusters in two .annot files (one in each hemisphere). There are also some ''*.cluster.summary'' files in this directory. Reading these files, I see the smallest clusters are about 120mm<sup>2</sup>. I would like to subdivide the larger clusters so that they are all between about 100-150mm<sup>2</sup>. I load the corresponding .annot file in Freesurfer just to verify the cluster names (the summary file lists 10 clusters, but the names do not follow a consistent naming convention). From the file, I see that clusters 1,2,3,4,6 and 8 need to be subdivided. Simple division by the desired cluster size tells me the number of divisions I want for each cluster:

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	Note: the first time I ran this, I have no idea where the rh.functional_subclusters.annot file went! Running the lh and re-running the rh subparcellation generated the expected files in the fsaverage/label directory.		Note: the first time I ran this, I have no idea where the rh.functional_subclusters.annot file went! Running the lh and re-running the rh subparcellation generated the expected files in the fsaverage/label directory.

	=== Check Subparcellation ===		== Check Subparcellation ==
	Presumably the python wrapper does this iteratively because all subdivisions are done along the same axis. As I discovered, a large number of subdivisions may be realized as a series of thin bands (below). In this case, it might be best to subdivide larger regions over a series of calls, as I describe below.		Presumably the python wrapper does this iteratively because all subdivisions are done along the same axis. As I discovered, a large number of subdivisions may be realized as a series of thin bands (below). In this case, it might be best to subdivide larger regions over a series of calls, as I describe below.

Chris: /* Transfer Subparcellation to Other Subjects */

2019-06-05T21:09:41Z

Transfer Subparcellation to Other Subjects

← Older revision		Revision as of 17:09, 5 June 2019
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	You may want to pull out overlapping voxels for T1 and T2 data (like a venn diagram) before mapping the surfaces to each subject, [http://ccnlab.psy.buffalo.edu/wiki/index.php/Working_with_ROIs_(Freesurfer) here].		You may want to pull out overlapping voxels for T1 and T2 data (like a venn diagram) before mapping the surfaces to each subject, [http://ccnlab.psy.buffalo.edu/wiki/index.php/Working_with_ROIs_(Freesurfer) here].

	'''Note: If you are working in ''fsaverage'' space for all participants, you only have to subparcellate your annotations once -- for the fsaverage surface.'''		'''Note: If you are working in ''fsaverage'' space for all participants, you only have to subparcellate your annotations once -- for the fsaverage surface.''' Because the functional analyses are invariably carried out in fsaverage space in order to compute group-level statistics, you will seldom have to transfer a subparcellation to a specific participant's surface space.

	[[Category: FreeSurfer]]		[[Category: FreeSurfer]]
	[[Category: Network Analyses]]		[[Category: Network Analyses]]

Chris: /* Transfer Subparcellation to Other Subjects */

2019-06-05T21:07:20Z

Transfer Subparcellation to Other Subjects

← Older revision		Revision as of 17:07, 5 June 2019
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	== Transfer Subparcellation to Other Subjects ==		== Transfer Subparcellation to Other Subjects ==
	Once satisfied with the source subparcellation, the scheme can be mapped to other surfaces using mri_surf2surf if, for example, you are working in '''self''' space (this needs to be done individually for the lh and rh surfaces -- below is an example command for the left):		Once satisfied with the source subparcellation, the scheme ''can'' be mapped to other surfaces using mri_surf2surf if, for example, you are working in '''self''' space (this needs to be done individually for the lh and rh surfaces -- below is an example command for the left):

	mri_surf2surf \		mri_surf2surf \

Chris: /* Transfer Subparcellation to Other Subjects */

2019-06-05T21:06:31Z

Transfer Subparcellation to Other Subjects

← Older revision		Revision as of 17:06, 5 June 2019
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	== Transfer Subparcellation to Other Subjects ==		== Transfer Subparcellation to Other Subjects ==
	Once satisfied with the source subparcellation, the scheme can be mapped to other surfaces using mri_surf2surf (this needs to be done individually for the lh and rh surfaces -- below is an example command for the left):		Once satisfied with the source subparcellation, the scheme can be mapped to other surfaces using mri_surf2surf if, for example, you are working in '''self''' space (this needs to be done individually for the lh and rh surfaces -- below is an example command for the left):

	mri_surf2surf \		mri_surf2surf \
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	You may want to pull out overlapping voxels for T1 and T2 data (like a venn diagram) before mapping the surfaces to each subject, [http://ccnlab.psy.buffalo.edu/wiki/index.php/Working_with_ROIs_(Freesurfer) here].		You may want to pull out overlapping voxels for T1 and T2 data (like a venn diagram) before mapping the surfaces to each subject, [http://ccnlab.psy.buffalo.edu/wiki/index.php/Working_with_ROIs_(Freesurfer) here].

			'''Note: If you are working in ''fsaverage'' space for all participants, you only have to subparcellate your annotations once -- for the fsaverage surface.'''

	[[Category: FreeSurfer]]		[[Category: FreeSurfer]]
	[[Category: Network Analyses]]		[[Category: Network Analyses]]

128.205.172.22: /* Iterative Subparcellation */

2017-11-14T17:51:28Z

Iterative Subparcellation

← Older revision		Revision as of 13:51, 14 November 2017
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	200 200functional_subclusters		200 200functional_subclusters

	~~The resulting subparcellations are much~~ less elongated.		Because each call to <code>mris_divide_parcellation</code> bisects the region along it's longest axis, successive function calls at each iteration produce increasingly less elongated subparcellations.

	== Transfer Subparcellation to Other Subjects ==		== Transfer Subparcellation to Other Subjects ==

128.205.172.22: /* Check Subparcellation */

2017-11-14T17:48:24Z

Check Subparcellation

← Older revision		Revision as of 13:48, 14 November 2017
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	=== Check Subparcellation ===		=== Check Subparcellation ===
	Presumably the python wrapper does this iteratively because all subdivisions are done along the same axis. As I discovered, a large number of subdivisions may be realized as a series of thin bands (below). In this case, it might be best to subdivide larger regions over a series of calls.		Presumably the python wrapper does this iteratively because all subdivisions are done along the same axis. As I discovered, a large number of subdivisions may be realized as a series of thin bands (below). In this case, it might be best to subdivide larger regions over a series of calls, as I describe below.

	[[File:Striped_Parcellation.png]]		[[File:Striped_Parcellation.png]]

192.168.1.1 at 18:49, 28 September 2017

2017-09-28T18:49:58Z

← Older revision		Revision as of 14:49, 28 September 2017
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	You may want to pull out overlapping voxels for T1 and T2 data (like a venn diagram) before mapping the surfaces to each subject, [http://ccnlab.psy.buffalo.edu/wiki/index.php/Working_with_ROIs_(Freesurfer) here].		You may want to pull out overlapping voxels for T1 and T2 data (like a venn diagram) before mapping the surfaces to each subject, [http://ccnlab.psy.buffalo.edu/wiki/index.php/Working_with_ROIs_(Freesurfer) here].

			[[Category: FreeSurfer]]
	[[Category: Network Analyses]]		[[Category: Network Analyses]]

128.205.173.202: /* Transfer Subparcellation to Other Subjects */

2017-07-27T20:54:16Z

Transfer Subparcellation to Other Subjects

← Older revision		Revision as of 16:54, 27 July 2017
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	--tval $SUBJECTS_DIR/FS_T1_501/label/lh.200functional_subclusters.annot		--tval $SUBJECTS_DIR/FS_T1_501/label/lh.200functional_subclusters.annot

	''Pro Tip: Use a global variable (e.g. SUBN) and use $SUBN in place of your subject in trgsubject and tval. Better yet, use the clustmap shell script.''		''Pro Tip: Use a global variable (e.g. SUBN) and use $SUBN in place of your subject in trgsubject and tval. Better yet, use the clustmap.sh shell script.''

	You may want to pull out overlapping voxels for T1 and T2 data (like a venn diagram) before mapping the surfaces to each subject, [http://ccnlab.psy.buffalo.edu/wiki/index.php/Working_with_ROIs_(Freesurfer) here].		You may want to pull out overlapping voxels for T1 and T2 data (like a venn diagram) before mapping the surfaces to each subject, [http://ccnlab.psy.buffalo.edu/wiki/index.php/Working_with_ROIs_(Freesurfer) here].

	[[Category: Network Analyses]]		[[Category: Network Analyses]]

128.205.173.202: /* Transfer Subparcellation to Other Subjects */

2017-07-27T20:53:54Z

Transfer Subparcellation to Other Subjects

← Older revision		Revision as of 16:53, 27 July 2017
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	--tval $SUBJECTS_DIR/FS_T1_501/label/lh.200functional_subclusters.annot		--tval $SUBJECTS_DIR/FS_T1_501/label/lh.200functional_subclusters.annot

	Pro Tip: Use a global variable (e.g. SUBN) and use $SUBN in place of your subject in trgsubject and tval.		''Pro Tip: Use a global variable (e.g. SUBN) and use $SUBN in place of your subject in trgsubject and tval. Better yet, use the clustmap shell script.''

	You may want to pull out overlapping voxels for T1 and T2 data (like a venn diagram) before mapping the surfaces to each subject, [http://ccnlab.psy.buffalo.edu/wiki/index.php/Working_with_ROIs_(Freesurfer) here].		You may want to pull out overlapping voxels for T1 and T2 data (like a venn diagram) before mapping the surfaces to each subject, [http://ccnlab.psy.buffalo.edu/wiki/index.php/Working_with_ROIs_(Freesurfer) here].

	[[Category: Network Analyses]]		[[Category: Network Analyses]]

128.205.173.202: /* Transfer Subparcellation to Other Subjects */

2017-07-26T19:39:26Z

Transfer Subparcellation to Other Subjects

← Older revision		Revision as of 15:39, 26 July 2017
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	--sval-annot $SUBJECTS_DIR/fsaverage/label/lh.200functional_subclusters.annot \		--sval-annot $SUBJECTS_DIR/fsaverage/label/lh.200functional_subclusters.annot \
	--tval $SUBJECTS_DIR/FS_T1_501/label/lh.200functional_subclusters.annot		--tval $SUBJECTS_DIR/FS_T1_501/label/lh.200functional_subclusters.annot

			Pro Tip: Use a global variable (e.g. SUBN) and use $SUBN in place of your subject in trgsubject and tval.

	You may want to pull out overlapping voxels for T1 and T2 data (like a venn diagram) before mapping the surfaces to each subject, [http://ccnlab.psy.buffalo.edu/wiki/index.php/Working_with_ROIs_(Freesurfer) here].		You may want to pull out overlapping voxels for T1 and T2 data (like a venn diagram) before mapping the surfaces to each subject, [http://ccnlab.psy.buffalo.edu/wiki/index.php/Working_with_ROIs_(Freesurfer) here].

	[[Category: Network Analyses]]		[[Category: Network Analyses]]