Producing Tables of Coordinates (SPM) - Revision history

192.168.1.1 at 17:15, 22 June 2016

2016-06-22T17:15:15Z

← Older revision		Revision as of 13:15, 22 June 2016
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	If you have many occurrences of the same anatomical region, you might use standard abbreviations (e.g., STG: Superior Temporal Gyrus; IFG: Inferior Frontal Gyrus) to make your tables more compact. These abbreviations should be listed in the table notes, even if they follow conventional usage.		If you have many occurrences of the same anatomical region, you might use standard abbreviations (e.g., STG: Superior Temporal Gyrus; IFG: Inferior Frontal Gyrus) to make your tables more compact. These abbreviations should be listed in the table notes, even if they follow conventional usage.

			[[Category: Manuscript Preparation]]

128.205.173.63: /* Sample Table */

2016-04-21T15:22:34Z

Sample Table

← Older revision		Revision as of 11:22, 21 April 2016
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	\| -3		\| -3
	\|-		\|-
	\| colspan="7" style="font-size: smaller; border-style: solid; border-width: 1px 0px 0px 0px;"\| Note: L, left; R, right; BA, Brodmann Area; Size, cluster size measured in voxels '; <br />FDR, FDR-corrected significance level ; <br />Max Z, maximum Z statistic reported for cluster. Coordinates reflect standard MNI space		\| colspan="7" style="font-size: smaller; border-style: solid; border-width: 1px 0px 0px 0px;"\| Note: L, left; R, right; BA, Brodmann Area; Size, cluster size measured in voxels; <br />FDR, FDR-corrected significance level ; <br />Max Z, maximum Z statistic reported for cluster. Coordinates reflect standard MNI space
	\|}		\|}

	If you have many occurrences of the same anatomical region, you might use standard abbreviations (e.g., STG: Superior Temporal Gyrus; IFG: Inferior Frontal Gyrus) to make your tables more compact. These abbreviations should be listed in the table notes, even if they follow conventional usage.		If you have many occurrences of the same anatomical region, you might use standard abbreviations (e.g., STG: Superior Temporal Gyrus; IFG: Inferior Frontal Gyrus) to make your tables more compact. These abbreviations should be listed in the table notes, even if they follow conventional usage.

128.205.173.63: /* Translating XYZ coordinates into Brain Regions */

2016-04-21T15:21:27Z

Translating XYZ coordinates into Brain Regions

← Older revision		Revision as of 11:21, 21 April 2016
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	In the UBFS /Scripts/Matlab folder are a pair of MATLAB files that look up sets of coordinates and report the corresponding Automated Anatomical Labeling (AAL) atlas regions. These will need to be in your MATLAB path. To find out if they are, open MATLAB and type		In the UBFS /Scripts/Matlab folder are a pair of MATLAB files that look up sets of coordinates and report the corresponding Automated Anatomical Labeling (AAL) atlas regions. These will need to be in your MATLAB path. To find out if they are, open MATLAB and type
	which aal_daemon		which aal_daemon
	If you get a 'not found' message, navigate to the ~/ubfs/cpmcnorg/Scripts/Matlab folder and copy aal_daemon.m and aal.mat to your ~/Documents/Matlab folder. You should now be able to run the aal_daemon function in MATLAB.		If you get a 'not found' message, navigate to the ~/ubfs/cpmcnorg/Scripts/Matlab folder and copy ''aal_daemon.m'' and ''aal.mat'' to your ~/Documents/Matlab folder. You should now be able to run the aal_daemon function in MATLAB.

	Try executing the following command in MATLAB, which will tell you how to use this function, and even give you some sample usage:		Try executing the following command in MATLAB, which will tell you how to use this function, and even give you some sample usage:

172.101.108.133: /* Sample Table */

2016-03-25T00:21:20Z

Sample Table

← Older revision		Revision as of 20:21, 24 March 2016
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	\|}		\|}

	If you have many occurrences of the same anatomical region, you might use standard abbreviations (e.g., STG: Superior Temporal Gyrus; IFG: Inferior Frontal Gyrus) to make your tables more compact. ~~Abbreviations~~ should be listed in the table notes.		If you have many occurrences of the same anatomical region, you might use standard abbreviations (e.g., STG: Superior Temporal Gyrus; IFG: Inferior Frontal Gyrus) to make your tables more compact. These abbreviations should be listed in the table notes, even if they follow conventional usage.

172.101.108.133: /* Translating XYZ coordinates into Brain Regions */

2016-03-25T00:19:48Z

Translating XYZ coordinates into Brain Regions

← Older revision		Revision as of 20:19, 24 March 2016
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	So here, you can see that the first triple of coordinates correspond to a point in the right superior temporal gyrus, or Brodmann Area 21.		So here, you can see that the first triple of coordinates correspond to a point in the right superior temporal gyrus, or Brodmann Area 21.

	Note that large clusters are likely to span multiple regions. You will have to use your good judgment to determine whether reporting a single brain region and/or Brodmann Area adequately describes the data. Also note that there is not a 1-to-1 correspondence between AAL region and Brodmann Area. For example, the Superior Temporal Gyrus (STG) includes ~~Brodmann Areas~~ 22, 41 and 42; immediately inferior to this is the Middle Temporal Gyrus (MTG), which includes BA 21. Because the function looks up the entry for a single point, this single entry may not be representative of the cluster in general. In these cases you may wish to do lookups on sub-peaks (see the sample table below for an instance where multiple BAs are listed for a single cluster).		Note that large clusters are likely to span multiple regions. You will have to use your good judgment to determine whether reporting a single brain region and/or Brodmann Area adequately describes the data. Also note that there is not a 1-to-1 correspondence between AAL region and Brodmann Area. For example, the Superior Temporal Gyrus (STG) traditionally includes BA 22, 41 and 42; immediately inferior to this is the Middle Temporal Gyrus (MTG), which traditionally includes BA 21. Because the function looks up the entry for a single point, this single entry may not be representative of the cluster in general, or may lead to an apparent mismatch between BA and anatomical label. In these cases you may wish to do lookups on sub-peaks (see the sample table below for an instance where multiple BAs are listed for a single cluster).

	== Generating the Table of Coordinates for a Manuscript ==		== Generating the Table of Coordinates for a Manuscript ==

172.101.108.133: /* Translating XYZ coordinates into Brain Regions */

2016-03-25T00:18:12Z

Translating XYZ coordinates into Brain Regions

← Older revision		Revision as of 20:18, 24 March 2016
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	So here, you can see that the first triple of coordinates correspond to a point in the right superior temporal gyrus, or Brodmann Area 21.		So here, you can see that the first triple of coordinates correspond to a point in the right superior temporal gyrus, or Brodmann Area 21.

	Note that large clusters are likely to span multiple regions. You will have to use your good judgment to determine whether reporting a single brain region and/or Brodmann Area adequately describes the data. Also note that there is not a 1-to-1 correspondence between AAL region and Brodmann Area. For example, the Superior Temporal Gyrus (STG) includes Brodmann Areas 21 ~~and 22~~. Because the function looks up the entry for a single point, this single entry may not be representative of the cluster in general. In these cases you may wish to do lookups on sub-peaks (see the sample table below for an instance where multiple BAs are listed for a single cluster).		Note that large clusters are likely to span multiple regions. You will have to use your good judgment to determine whether reporting a single brain region and/or Brodmann Area adequately describes the data. Also note that there is not a 1-to-1 correspondence between AAL region and Brodmann Area. For example, the Superior Temporal Gyrus (STG) includes Brodmann Areas 22, 41 and 42; immediately inferior to this is the Middle Temporal Gyrus (MTG), which includes BA 21. Because the function looks up the entry for a single point, this single entry may not be representative of the cluster in general. In these cases you may wish to do lookups on sub-peaks (see the sample table below for an instance where multiple BAs are listed for a single cluster).

	== Generating the Table of Coordinates for a Manuscript ==		== Generating the Table of Coordinates for a Manuscript ==

Chris: /* Obtaining the SPM Table of Coordinates */

2016-03-24T16:32:53Z

Obtaining the SPM Table of Coordinates

← Older revision		Revision as of 12:32, 24 March 2016
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	== Obtaining the SPM Table of Coordinates ==		== Obtaining the SPM Table of Coordinates ==
	'Note that the table of coordinates should be produced using ''identical'' parameters to those used to produce the brain renderings. This is most easily done by producing the table and the 3D contrast volume at the same time.'		'''Note that the table of coordinates should be produced using ''identical'' parameters to those used to produce the brain renderings. This is most easily done by producing the table and the 3D contrast volume at the same time.
			'''
	In SPM, load the contrast of interest		In SPM, load the contrast of interest
	#Select Results from the GUI interface		#Select Results from the GUI interface

Chris: /* Translating XYZ coordinates into Brain Regions */

2016-03-24T16:30:43Z

Translating XYZ coordinates into Brain Regions

← Older revision		Revision as of 12:30, 24 March 2016
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	Each entry of mytable contains the information for the corresponding coordinate triple in the order that you entered them into your coordlist matrix.		Each entry of mytable contains the information for the corresponding coordinate triple in the order that you entered them into your coordlist matrix.
	>>mytable{1}		>>mytable{1}
	ans:		ans=
	aal: Temporal_Sup_R		aal: Temporal_Sup_R
	ba: 21		ba: 21
	x: 63		x: 63
	y: -27		y: -27
	z: 3		z: 3

	So here, you can see that the first triple of coordinates correspond to a point in the right superior temporal gyrus, or Brodmann Area 21.		So here, you can see that the first triple of coordinates correspond to a point in the right superior temporal gyrus, or Brodmann Area 21.

Chris at 16:30, 24 March 2016

2016-03-24T16:30:13Z

← Older revision		Revision as of 12:30, 24 March 2016
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	You can (and should) save the SPM output to a postscript (.ps) file at this point. The .ps file can be opened in Adobe Acrobat Reader.		You can (and should) save the SPM output to a postscript (.ps) file at this point. The .ps file can be opened in Adobe Acrobat Reader.

			The SPM output has nearly all the information you will need to produce a table of coordinates for this contrast for a manuscript. The 3D coordinates are difficult to interpret, however, for someone without an encyclopaedic knowledge of brain taxonomy. The next step is to use a MATLAB script to translate the XYZ coordinates into user-friendly brain nomenclature.

			== Translating XYZ coordinates into Brain Regions ==
			In the UBFS /Scripts/Matlab folder are a pair of MATLAB files that look up sets of coordinates and report the corresponding Automated Anatomical Labeling (AAL) atlas regions. These will need to be in your MATLAB path. To find out if they are, open MATLAB and type
			which aal_daemon
			If you get a 'not found' message, navigate to the ~/ubfs/cpmcnorg/Scripts/Matlab folder and copy aal_daemon.m and aal.mat to your ~/Documents/Matlab folder. You should now be able to run the aal_daemon function in MATLAB.

			Try executing the following command in MATLAB, which will tell you how to use this function, and even give you some sample usage:
			help aal_daemon

			Pay particular attention to the sample usage, as this shows you how you will run it on your SPM output. Suppose, after thresholding your SPM data as described above, there were two major clusters, roughly on opposites sides of the brain. These clusters might have had peaks in the following locations:
			63,-27,3 and -57,-9,-3. Now you wish to determine what the corresponding brain regions are. The aal_daemon function will take those coordinate triples and look each of them up and report an anatomical brain region and Brodmann Area (another taxonomic naming system) for each location. You can look up the coordinates individually, or you can enter them all into a matrix and have the function look up all the coordinates at once (this is probably the fastest approach).

			First, you would make a matrix of coordinates. In this case, we have two triples of coordinates. MATLAB matrices separate columns with commas, and rows with semicolons. Each triple of coordinates is a single row in the matrix. So in our example, we might make a matrix called coordlist:
			coordlist=[63,-27,3;-57,-9,-3];
			Now you can save the results of the aal_daemon lookup to a cell array:
			mytable=aal_daemon(coordlist);

			Each entry of mytable contains the information for the corresponding coordinate triple in the order that you entered them into your coordlist matrix.
			>>mytable{1}
			ans:
			aal: Temporal_Sup_R
			ba: 21
			x: 63
			y: -27
			z: 3

			So here, you can see that the first triple of coordinates correspond to a point in the right superior temporal gyrus, or Brodmann Area 21.

			Note that large clusters are likely to span multiple regions. You will have to use your good judgment to determine whether reporting a single brain region and/or Brodmann Area adequately describes the data. Also note that there is not a 1-to-1 correspondence between AAL region and Brodmann Area. For example, the Superior Temporal Gyrus (STG) includes Brodmann Areas 21 and 22. Because the function looks up the entry for a single point, this single entry may not be representative of the cluster in general. In these cases you may wish to do lookups on sub-peaks (see the sample table below for an instance where multiple BAs are listed for a single cluster).

	== Generating the Table of Coordinates for a Manuscript ==		== Generating the Table of Coordinates for a Manuscript ==

Chris: /* Generating the Table of Coordinates for a Manuscript */

2016-03-24T16:01:04Z

Generating the Table of Coordinates for a Manuscript

← Older revision		Revision as of 12:01, 24 March 2016
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	\| colspan="7" style="font-style: italic; text-align: center;"\| Table data here		\| colspan="7" style="font-style: italic; text-align: center;"\| Table data here
	\|-		\|-
	\| colspan="7" style="font-size: smaller; border-style: solid; border-width: 1px 0px ~~1px~~ 0px;"\| Note: L, left; R, right; BA, Brodmann Area; Size, cluster size measured in voxels ''(or mm^3)''; <br />FDR, FDR-corrected significance level ''(used for SIG column; alternatively, FWE, Family-wise error corrected significance level)''; <br />Max Z, maximum Z statistic reported for cluster. Coordinates reflect standard MNI space		\| colspan="7" style="font-size: smaller; border-style: solid; border-width: 1px 0px 0px 0px;"\| Note: L, left; R, right; BA, Brodmann Area; Size, cluster size measured in voxels ''(or mm^3)''; <br />FDR, FDR-corrected significance level ''(used for SIG column; alternatively, FWE, Family-wise error corrected significance level)''; <br />Max Z, maximum Z statistic reported for cluster. Coordinates reflect standard MNI space
	\|}		\|}