AnchorBar - Revision history

Chris at 15:14, 14 September 2022

2022-09-14T15:14:54Z

← Older revision		Revision as of 11:14, 14 September 2022
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	AnchorBar_tools.py provides tools to list, rename and relabel annotations. Each annotation has a unique ID and descriptors indicating the hemisphere, a shortname used for naming labels generated from set operations, and a path indicating the file path of the source .annot file. The default set of annotations stored in '''annot.db''' includes the 10 pairs of lhrh annotations from fsaverage/label:		AnchorBar_tools.py provides tools to list, rename and relabel annotations. Each annotation has a unique ID and descriptors indicating the hemisphere, a shortname used for naming labels generated from set operations, and a path indicating the file path of the source .annot file. The default set of annotations stored in '''annot.db''' includes the 10 pairs of lhrh annotations from fsaverage/label:
	AnchorBar_tools.py --db annot.db --list		AnchorBar_tools.py --db annot.db --list
			The labels associated with a given annotation can be found using the <code>--labels</code> switch:
			#List all the labels in the lh.aparc_2009s.annot FreeSurfer annotation
			AnchorBar_tools.py --db annot.db --labels 2

	=Adding Annotations=		=Adding Annotations=

Chris: /* Merging (Union) of Two Annotations */

2022-09-14T15:10:39Z

Merging (Union) of Two Annotations

← Older revision		Revision as of 11:10, 14 September 2022
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	==Merging (Union) of Two Annotations==		==Merging (Union) of Two Annotations==
	Example: We have two tasks, A and B, and each task condition has been contrasted with rest (A vs Rest; B vs Rest). We wish to identify left-hemisphere regions that are involved in either task, so we compute the union. This functionality has been added to AnchorBar		Example: We have two tasks, A and B, and each task condition has been contrasted with rest (A vs Rest; B vs Rest). We wish to identify left-hemisphere regions that are involved in either task, so we compute the union. This functionality has been added to AnchorBar
	#Assumes that lh.AnnotA and lh.AnnotB correspond to the annotations derived from the two task contrasts, A vs Rest and B vs Rest, respectively		#Assumes that lh.AnnotA and lh.AnnotB correspond to the annotations derived from the two task contrasts,
	#and that these annotations are numbered 23 and 25		#A vs Rest and B vs Rest, respectively, and that these annotations are numbered 23 and 25
	AnchorBar_sets.py --db annot.db --union 23 25		AnchorBar_sets.py --db annot.db --union 23 25

Chris: /* Merging (Union) of Two Annotations */

2022-09-14T15:10:20Z

Merging (Union) of Two Annotations

← Older revision		Revision as of 11:10, 14 September 2022
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	==Merging (Union) of Two Annotations==		==Merging (Union) of Two Annotations==
	Example: We have two tasks, A and B, and each task condition has been contrasted with rest (A vs Rest; B vs Rest). We wish to identify left-hemisphere regions that are involved in either task, so we compute the union. This functionality has been added to AnchorBar		Example: We have two tasks, A and B, and each task condition has been contrasted with rest (A vs Rest; B vs Rest). We wish to identify left-hemisphere regions that are involved in either task, so we compute the union. This functionality has been added to AnchorBar
	#Assumes that lh.AnnotA and lh.AnnotB correspond to the annotations derived from the two task contrasts, A and B, respectively		#Assumes that lh.AnnotA and lh.AnnotB correspond to the annotations derived from the two task contrasts, A vs Rest and B vs Rest, respectively
	#and that these annotations are numbered 23 and 25		#and that these annotations are numbered 23 and 25
	AnchorBar_sets.py --db annot.db --union 23 25		AnchorBar_sets.py --db annot.db --union 23 25

Chris: /* Merging (Union) of Two Annotations */

2022-09-14T15:09:52Z

Merging (Union) of Two Annotations

← Older revision		Revision as of 11:09, 14 September 2022
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	Example: We have two tasks, A and B, and each task condition has been contrasted with rest (A vs Rest; B vs Rest). We wish to identify left-hemisphere regions that are involved in either task, so we compute the union. This functionality has been added to AnchorBar		Example: We have two tasks, A and B, and each task condition has been contrasted with rest (A vs Rest; B vs Rest). We wish to identify left-hemisphere regions that are involved in either task, so we compute the union. This functionality has been added to AnchorBar
	#Assumes that lh.AnnotA and lh.AnnotB correspond to the annotations derived from the two task contrasts, A and B, respectively		#Assumes that lh.AnnotA and lh.AnnotB correspond to the annotations derived from the two task contrasts, A and B, respectively
	#and that these annotations are numbered 14 and 15		#and that these annotations are numbered 23 and 25
	AnchorBar_sets.py --db annot.db --union ~~14 15~~		AnchorBar_sets.py --db annot.db --union 23 25

Chris: /* Merging (Union) of Two Annotations */

2022-09-14T15:09:04Z

Merging (Union) of Two Annotations

← Older revision		Revision as of 11:09, 14 September 2022
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	==Merging (Union) of Two Annotations==		==Merging (Union) of Two Annotations==
	Example: We have two tasks, A and B, and each task condition has been contrasted with rest (A vs Rest; B vs Rest). We wish to identify regions that are involved in either task, so we compute the union.		Example: We have two tasks, A and B, and each task condition has been contrasted with rest (A vs Rest; B vs Rest). We wish to identify left-hemisphere regions that are involved in either task, so we compute the union. This functionality has been added to AnchorBar
	~~Unfortunately~~, ~~it looks like I have to write this functionality!~~		#Assumes that lh.AnnotA and lh.AnnotB correspond to the annotations derived from the two task contrasts, A and B, respectively
			#and that these annotations are numbered 14 and 15
			AnchorBar_sets.py --db annot.db --union 14 15

Chris: /* Set Operations on Annotations */

2022-08-17T21:48:03Z

Set Operations on Annotations

← Older revision		Revision as of 17:48, 17 August 2022
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	=Set Operations on Annotations=		=Set Operations on Annotations=
			Note that all set operations require pairs of annotations from the same hemisphere. If unsure, list the annotations and take careful note of the hemisphere noted for the ids of the annotations you're interested in. Using annotations from opposite hemispheres will result in an error message and produce no new output.

	==Intersection of Two Annotations==		==Intersection of Two Annotations==
	Example: We have a functional contrast (A vs Rest) and wish to divide the large clusters along Brodmann Area boundaries. By intersecting the clusters (which only cover some of the brain surface) with one of the anatomical atlas annotations (which cover all of the brain surface), we assign a new label to each vertex according to which cluster and which anatomical label it corresponds to. Vertices not belonging to functional clusters will be dropped. The end result is a new annotation where the clusters are subdivided along anatomical boundaries.		Example: We have a functional contrast (A vs Rest) and wish to divide the large clusters along Brodmann Area boundaries. By intersecting the clusters (which only cover some of the brain surface) with one of the anatomical atlas annotations (which cover all of the brain surface), we assign a new label to each vertex according to which cluster and which anatomical label it corresponds to. Vertices not belonging to functional clusters will be dropped. The end result is a new annotation where the clusters are subdivided along anatomical boundaries.

Chris: /* Intersection of Two Annotations */

2022-08-17T21:44:13Z

Intersection of Two Annotations

← Older revision		Revision as of 17:44, 17 August 2022
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	==Intersection of Two Annotations==		==Intersection of Two Annotations==
	Example: We have a functional contrast (A vs Rest) and wish to divide the large clusters along Brodmann Area boundaries. By intersecting the clusters (which only cover some of the brain surface) with one of the anatomical atlas annotations (which cover all of the brain surface), we assign a new label to each vertex according to which cluster and which anatomical label it corresponds to. Vertices not belonging to functional clusters will be dropped. The end result is a new annotation where the clusters are subdivided along anatomical boundaries.		Example: We have a functional contrast (A vs Rest) and wish to divide the large clusters along Brodmann Area boundaries. By intersecting the clusters (which only cover some of the brain surface) with one of the anatomical atlas annotations (which cover all of the brain surface), we assign a new label to each vertex according to which cluster and which anatomical label it corresponds to. Vertices not belonging to functional clusters will be dropped. The end result is a new annotation where the clusters are subdivided along anatomical boundaries.

	We first list the annotations in the database to find the corresponding id numbers. A vs Rest are annotations 23 (lh) and 24 (rh), and the Brodmann annotations are 5 (lh) and 15 (rh). We intersect the two corresponding annotations thus:		We first list the annotations in the database to find the corresponding id numbers. A vs Rest are annotations 23 (lh) and 24 (rh), and the Brodmann annotations are 5 (lh) and 15 (rh). We intersect the two corresponding annotations thus:
	AnchorBar_sets.py --db annot.db --intersect 5 23		AnchorBar_sets.py --db annot.db --intersect 5 23

Chris: /* Intersection of Two Annotations */

2022-08-17T21:37:16Z

Intersection of Two Annotations

← Older revision		Revision as of 17:37, 17 August 2022
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	We first list the annotations in the database to find the corresponding id numbers. A vs Rest are annotations 23 (lh) and 24 (rh), and the Brodmann annotations are 5 (lh) and 15 (rh). We intersect the two corresponding annotations thus:		We first list the annotations in the database to find the corresponding id numbers. A vs Rest are annotations 23 (lh) and 24 (rh), and the Brodmann annotations are 5 (lh) and 15 (rh). We intersect the two corresponding annotations thus:
	AnchorBar_sets.py --db annot.db --intersect 5 23		AnchorBar_sets.py --db annot.db --intersect 5 23
	AnchorBar_sets.py --db annot.db --intersect 15 24		AnchorBar_sets.py --db annot.db --intersect 15 24

	==Merging (Union) of Two Annotations==		==Merging (Union) of Two Annotations==
	Example: We have two tasks, A and B, and each task condition has been contrasted with rest (A vs Rest; B vs Rest). We wish to identify regions that are involved in either task, so we compute the union.		Example: We have two tasks, A and B, and each task condition has been contrasted with rest (A vs Rest; B vs Rest). We wish to identify regions that are involved in either task, so we compute the union.
	Unfortunately, it looks like I have to write this functionality!		Unfortunately, it looks like I have to write this functionality!

Chris at 21:36, 17 August 2022

2022-08-17T21:36:58Z

← Older revision		Revision as of 17:36, 17 August 2022
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	25 lh AvsB /home/projects/mystudy/fsaverage/label		25 lh AvsB /home/projects/mystudy/fsaverage/label
	26 rh AvsB /home/projects/mystudy/fsaverage/label		26 rh AvsB /home/projects/mystudy/fsaverage/label

			=Set Operations on Annotations=
			==Intersection of Two Annotations==
			Example: We have a functional contrast (A vs Rest) and wish to divide the large clusters along Brodmann Area boundaries. By intersecting the clusters (which only cover some of the brain surface) with one of the anatomical atlas annotations (which cover all of the brain surface), we assign a new label to each vertex according to which cluster and which anatomical label it corresponds to. Vertices not belonging to functional clusters will be dropped. The end result is a new annotation where the clusters are subdivided along anatomical boundaries.
			We first list the annotations in the database to find the corresponding id numbers. A vs Rest are annotations 23 (lh) and 24 (rh), and the Brodmann annotations are 5 (lh) and 15 (rh). We intersect the two corresponding annotations thus:
			AnchorBar_sets.py --db annot.db --intersect 5 23
			AnchorBar_sets.py --db annot.db --intersect 15 24

			==Merging (Union) of Two Annotations==
			Example: We have two tasks, A and B, and each task condition has been contrasted with rest (A vs Rest; B vs Rest). We wish to identify regions that are involved in either task, so we compute the union.
			Unfortunately, it looks like I have to write this functionality!

Chris: /* Requirements */

2022-08-17T21:19:30Z

Requirements

← Older revision		Revision as of 17:19, 17 August 2022
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	AnchorBar (aka "Analyzer") is a Python program developed to maintain and compute set operations on FreeSurfer annotation files. It's kind of like SPM's MarsBar plugin, but for FreeSurfer.		AnchorBar (aka "Analyzer") is a Python program developed to maintain and compute set operations on FreeSurfer annotation files. It's kind of like SPM's MarsBar plugin, but for FreeSurfer.
	=Requirements=		=Requirements=
	AnchorBar has a few dependencies that ~~must~~ be ~~met~~:		AnchorBar has a few dependencies that might not be part of your base Python install:
	~~#argparse~~		*hashlib
	~~#sqlite3~~		*nibabel
	#hashlib
	#nibabel
	~~#random~~
	~~#numpy~~
	Attempting to run the scripts will fail and report missing libraries. They can be installed using pip:		Attempting to run the scripts will fail and report missing libraries. They can be installed using pip:
	pip install nibabel		pip install nibabel
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	usage: AnchorBar_tools.py [-h] [--list] [--labels annot_id] [--db DB] [--rename annot_id new_shortname]		usage: AnchorBar_tools.py [-h] [--list] [--labels annot_id] [--db DB] [--rename annot_id new_shortname]
	[--relabel annot_id label_id new_label_name] [--abbrev annot_id label_id abbrev_label_name]		[--relabel annot_id label_id new_label_name] [--abbrev annot_id label_id abbrev_label_name]

	=Querying Available Annotations=		=Querying Available Annotations=
	AnchorBar_tools.py provides tools to list, rename and relabel annotations. Each annotation has a unique ID and descriptors indicating the hemisphere, a shortname used for naming labels generated from set operations, and a path indicating the file path of the source .annot file. The default set of annotations stored in '''annot.db''' includes the 10 pairs of lhrh annotations from fsaverage/label:		AnchorBar_tools.py provides tools to list, rename and relabel annotations. Each annotation has a unique ID and descriptors indicating the hemisphere, a shortname used for naming labels generated from set operations, and a path indicating the file path of the source .annot file. The default set of annotations stored in '''annot.db''' includes the 10 pairs of lhrh annotations from fsaverage/label: