Lausanne Parcellation - Revision history

128.205.173.88: /* Working in FSAVERAGE Space */

2018-01-31T18:50:23Z

Working in FSAVERAGE Space

← Older revision		Revision as of 14:50, 31 January 2018
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	== Working in FSAVERAGE Space ==		== Working in FSAVERAGE Space ==
	If you have prepocessed your subject's BOLD data in '''fsaverage''' space (e.g., to also facilitate a group-level GLM analysis) you can take advantage of the subparcellations that have been mapped to fsaverage. The original subparcellations came from participant 0183 from the Semantic Imagery experiment. The shell script <code>cpannot.sh</code> (found in the ubfs Scripts/Shell folder) was used to translate that subject's subparcellation to fsaverage space (which, after all, was used to determine the initial coarse parcellation of that participant in the first place!). The lausanne annotation files may not exist in the fsaverage/label/ folder on your computer. If this is the case, they can be copied from '''ubfs/Software/fsaverage_lausanne.tgz''' to '''$SUBJECTS_DIR/fsaverage/label''' where they can be unzipped. You may run in to write permission problems when trying to copy new files into this folder, depending on whether ~~the~~ fsaverage ~~directory~~ is a copy (should be no problem) or a symbolic link (possible problem) to $FREESURFER_HOME/subjects/fsaverage.		If you have prepocessed your subject's BOLD data in '''fsaverage''' space (e.g., to also facilitate a group-level GLM analysis) you can take advantage of the subparcellations that have been mapped to fsaverage. The original subparcellations came from participant 0183 from the Semantic Imagery experiment. The shell script <code>cpannot.sh</code> (found in the ubfs Scripts/Shell folder) was used to translate that subject's subparcellation to fsaverage space (which, after all, was used to determine the initial coarse parcellation of that participant in the first place!). The lausanne annotation files may not exist in the fsaverage/label/ folder on your computer. If this is the case, they can be copied from '''ubfs/Software/fsaverage_lausanne.tgz''' to '''$SUBJECTS_DIR/fsaverage/label''' where they can be unzipped. You may run in to write permission problems when trying to copy new files into this folder, depending on whether $SUBJECTS_DIR/fsaverage is a copy (should be no problem) or a symbolic link (possible problem) to $FREESURFER_HOME/subjects/fsaverage.

	== Working in Self Space ==		== Working in Self Space ==

128.205.173.88: /* Working in FSAVERAGE Space */

2018-01-31T18:49:44Z

Working in FSAVERAGE Space

← Older revision		Revision as of 14:49, 31 January 2018
Line 4:		Line 4:

	== Working in FSAVERAGE Space ==		== Working in FSAVERAGE Space ==
	If you have prepocessed your subject's BOLD data in '''fsaverage''' space (e.g., to also facilitate a group-level GLM analysis) you can take advantage of the subparcellations that have been mapped to fsaverage. The original subparcellations came from participant 0183 from the Semantic Imagery experiment. The shell script <code>cpannot.sh</code> (found in the ubfs Scripts/Shell folder) was used to translate that subject's subparcellation to fsaverage space (which, after all, was used to determine the initial coarse parcellation of that participant in the first place!). The lausanne annotation files may not exist in the fsaverage/label/ folder on your computer. If ~~not~~, they can be copied from '''ubfs/Software/fsaverage_lausanne.tgz''' to '''$SUBJECTS_DIR/fsaverage/label''' where they can be unzipped.		If you have prepocessed your subject's BOLD data in '''fsaverage''' space (e.g., to also facilitate a group-level GLM analysis) you can take advantage of the subparcellations that have been mapped to fsaverage. The original subparcellations came from participant 0183 from the Semantic Imagery experiment. The shell script <code>cpannot.sh</code> (found in the ubfs Scripts/Shell folder) was used to translate that subject's subparcellation to fsaverage space (which, after all, was used to determine the initial coarse parcellation of that participant in the first place!). The lausanne annotation files may not exist in the fsaverage/label/ folder on your computer. If this is the case, they can be copied from '''ubfs/Software/fsaverage_lausanne.tgz''' to '''$SUBJECTS_DIR/fsaverage/label''' where they can be unzipped. You may run in to write permission problems when trying to copy new files into this folder, depending on whether the fsaverage directory is a copy (should be no problem) or a symbolic link (possible problem) to $FREESURFER_HOME/subjects/fsaverage.

	== Working in Self Space ==		== Working in Self Space ==

128.205.173.88 at 18:47, 31 January 2018

2018-01-31T18:47:04Z

← Older revision		Revision as of 14:47, 31 January 2018
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	The Lausanne 2008 parcellation scheme refers to the 2008 PLoS Biology Paper [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060159 Mapping the Structural Core of Human Cerebral Cortex]		The Lausanne 2008 parcellation scheme refers to the 2008 PLoS Biology Paper [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060159 Mapping the Structural Core of Human Cerebral Cortex]

	== ~~Lausanne Parcellation Workflow~~ ==		== Working in FSAVERAGE Space ==
			If you have prepocessed your subject's BOLD data in '''fsaverage''' space (e.g., to also facilitate a group-level GLM analysis) you can take advantage of the subparcellations that have been mapped to fsaverage. The original subparcellations came from participant 0183 from the Semantic Imagery experiment. The shell script <code>cpannot.sh</code> (found in the ubfs Scripts/Shell folder) was used to translate that subject's subparcellation to fsaverage space (which, after all, was used to determine the initial coarse parcellation of that participant in the first place!). The lausanne annotation files may not exist in the fsaverage/label/ folder on your computer. If not, they can be copied from '''ubfs/Software/fsaverage_lausanne.tgz''' to '''$SUBJECTS_DIR/fsaverage/label''' where they can be unzipped.

			== Working in Self Space ==
			If you wish to use subparcellated brain regions on BOLD data preprocessed in a subject's '''self''' space, it will be necessary for you to subparcellate each subject's regional definitions individually. This follows the workflow described below:

	=== Recon-all ===		=== Recon-all ===
	A precondition for subparcellating the cortex in surface space is that you will first require a parcellated cortical surface mesh on which to operate. You will need to take a T1 (i.e., anatomical; MPRAGE) volume to the end of the recon-all pipeline, by running the autorecon1, autorecon2 and autorecon3 steps, as outlined elsewhere.		A precondition for subparcellating the cortex in surface space is that you will first require a parcellated cortical surface mesh on which to operate. You will need to take a T1 (i.e., anatomical; MPRAGE) volume to the end of the recon-all pipeline, by running the autorecon1, autorecon2 and autorecon3 steps, as outlined elsewhere.

64.134.64.103: /* From the Linux Terminal */

2016-06-14T20:24:14Z

From the Linux Terminal

← Older revision		Revision as of 16:24, 14 June 2016
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	Now you should be able to run the script from the shell terminal:		Now you should be able to run the script from the shell terminal:
	~~SUBJECT_ID=FS_T1_501~~
	subpar.py ~~$SUBJECT_ID~~		subpar.py FS_T1_501

	==== Using the iPython Interactive Shell ====		==== Using the iPython Interactive Shell ====

172.101.108.133: /* Subparcellate Using ConnectomeMapper in Python */

2016-06-13T22:21:01Z

Subparcellate Using ConnectomeMapper in Python

← Older revision		Revision as of 18:21, 13 June 2016
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	Next, use the <code>cd</code> command to navigate into the subject folder.		Next, use the <code>cd</code> command to navigate into the subject folder.
	cd FS_T1_501		cd FS_T1_501
			==== From the Linux Terminal ====
			A handy dandy python script has been written to use the CMTK python interface. It can be found in the ubfs Scripts/Python directory. If it is not already in your linux path, copy it:
			cp ~/ubfs/cpmcnorg/Scripts/Python/subpar.py ~/bin/

	~~Next~~, ~~launch~~ ipython in your terminal window:		Now you should be able to run the script from the shell terminal:
			SUBJECT_ID=FS_T1_501
			subpar.py $SUBJECT_ID

			==== Using the iPython Interactive Shell ====
			The subpar.py script described above automates the python commands described in this section. If, for whatever reason, you wish to run these steps in iPython, you will begin by launching ipython in your terminal window:
	ipython		ipython

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	In [1]:		In [1]:

	Suppose you wish to sub-parcellate the subject with ID FS_T1_501. You would type the following commands in the interactive Python shell:		Suppose you wish to sub-parcellate the subject with ID FS_T1_501. You would type the following commands in the interactive Python shell ('''In [?]:''' at the start of each line is the iPython command prompt, and does not need to be typed):
	import os		In [1]: import os
	import nipype.interfaces.cmtk as cmtk		In [2]: import nipype.interfaces.cmtk as cmtk
	parcellate = cmtk.Parcellate()		In [3]: parcellate = cmtk.Parcellate()
	parcellate.inputs.subject_id="FS_T1_501"		In [4]: parcellate.inputs.subject_id="FS_T1_501"
	parcellate.inputs.subjects_dir=os.environ['SUBJECTS_DIR'];		In [5]: parcellate.inputs.subjects_dir=os.environ['SUBJECTS_DIR'];
	parcellate.run();		In [6]: parcellate.run();

	That's it. If you had a different participant in mind, you would simply provide a different folder name for the <code>parcellate.inputs.subject_id</code> value.		That's it. If you had a different participant in mind, you would simply provide a different folder name for the <code>parcellate.inputs.subject_id</code> value.

			Whether you use the <code>subpar.py</code> script, or run the steps in iPython, the parcellation step will run for quite a while.
	~~Alternatively, copy~~ the ~~handy-dandy~~ <code>subpar.py</code> script ~~into your ~/bin from ~/ubfs/cpmcnorg/Scripts/Python~~
	~~cp ~/ubfs/cpmcnorg/Scripts/Python/subpar.py ~/bin/~~

	~~Now you can <code>cd</code> into <code>$SUBJECTS_DIR/FS_T1_501</code> and~~ run the ~~python script with your subject folder name.~~
	~~subpar.py FS_T1_501~~

	~~The~~ parcellation step will run for quite a while.
	==== Output ====		==== Output ====
	When it has finished, the resulting label files can be found in multiple subdirectories of ''${SUBJECTS_DIR}/${SUBJECT_ID}/label/''. Look for subdirectories named ''regenerated_?h_###'', where '?h' will be either lh or rh, and '###' is one of the numbers 36, 60, 125, 250 and 500 (the numbers representing the numbers of regions in each subparcellation, roughly doubling each time).		When it has finished, the resulting label files can be found in multiple subdirectories of ''${SUBJECTS_DIR}/${SUBJECT_ID}/label/''. Look for subdirectories named ''regenerated_?h_###'', where '?h' will be either lh or rh, and '###' is one of the numbers 36, 60, 125, 250 and 500 (the numbers representing the numbers of regions in each subparcellation, roughly doubling each time).

128.205.173.202 at 21:08, 25 May 2016

2016-05-25T21:08:17Z

← Older revision		Revision as of 17:08, 25 May 2016
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	That's it. If you had a different participant in mind, you would simply provide a different folder name for the <code>parcellate.inputs.subject_id</code> value.		That's it. If you had a different participant in mind, you would simply provide a different folder name for the <code>parcellate.inputs.subject_id</code> value.

	Alternatively, copy the subpar.py script into your ~/bin from ~/ubfs/cpmcnorg/Scripts/Python
			Alternatively, copy the handy-dandy <code>subpar.py</code> script into your ~/bin from ~/ubfs/cpmcnorg/Scripts/Python
	cp ~/ubfs/cpmcnorg/Scripts/Python/subpar.py ~/bin/		cp ~/ubfs/cpmcnorg/Scripts/Python/subpar.py ~/bin/

128.205.173.202 at 20:58, 25 May 2016

2016-05-25T20:58:12Z

← Older revision		Revision as of 16:58, 25 May 2016
Line 43:		Line 43:

	Alternatively, copy the subpar.py script into your ~/bin from ~/ubfs/cpmcnorg/Scripts/Python		Alternatively, copy the subpar.py script into your ~/bin from ~/ubfs/cpmcnorg/Scripts/Python
	cd		cp ~/ubfs/cpmcnorg/Scripts/Python/subpar.py ~/bin/

			Now you can <code>cd</code> into <code>$SUBJECTS_DIR/FS_T1_501</code> and run the python script with your subject folder name.
			subpar.py FS_T1_501

	The parcellation step will run for quite a while.		The parcellation step will run for quite a while.

128.205.173.202 at 20:53, 25 May 2016

2016-05-25T20:53:44Z

← Older revision		Revision as of 16:53, 25 May 2016
Line 41:		Line 41:

	That's it. If you had a different participant in mind, you would simply provide a different folder name for the <code>parcellate.inputs.subject_id</code> value.		That's it. If you had a different participant in mind, you would simply provide a different folder name for the <code>parcellate.inputs.subject_id</code> value.

			Alternatively, copy the subpar.py script into your ~/bin from ~/ubfs/cpmcnorg/Scripts/Python
			cd

	The parcellation step will run for quite a while.		The parcellation step will run for quite a while.
	==== Output ====		==== Output ====

128.205.173.202 at 19:31, 25 May 2016

2016-05-25T19:31:36Z

← Older revision		Revision as of 15:31, 25 May 2016
Line 1:		Line 1:
	The Lausanne Parcellation is a workflow that subdivides the 30+ general brain regions into many smaller partitions of approximately equal size. This gives us a finer-grained partitioning of the cortex. Because they are smaller, these partitions are more likely to behave relatively more homogeneously during a particular task. ~~Becaues~~ they are of comparable size, it is more justifiable to weight them equally in your analyses.		The Lausanne Parcellation is a workflow that subdivides the 30+ general brain regions into many smaller partitions of approximately equal size. This gives us a finer-grained partitioning of the cortex. Because they are smaller, these partitions are more likely to behave relatively more homogeneously during a particular task. Because they are of comparable size, it is more justifiable to weight them equally in your analyses.

	The Lausanne 2008 parcellation scheme refers to the 2008 PLoS Biology Paper [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060159 Mapping the Structural Core of Human Cerebral Cortex]		The Lausanne 2008 parcellation scheme refers to the 2008 PLoS Biology Paper [http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060159 Mapping the Structural Core of Human Cerebral Cortex]

172.101.108.133: /* Run the Scripts */

2016-05-13T16:00:58Z

Run the Scripts

← Older revision		Revision as of 12:00, 13 May 2016
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	clut.sh 501_001		clut.sh 501_001

	Note that this script will use the $SUBJECTS_DIR environment variable to figure out where to start looking for the files. Your terminal window may be using the default Freesurfer directory for this value, and so you may have to first change the $SUBJECTS_DIR environment variable to the directory containing ''your'' data.		Note that this script will use the '''$SUBJECTS_DIR''' environment variable to figure out where to start looking for the files. Your terminal window may be using the default Freesurfer directory for this value, and so you may have to first change the '''$SUBJECTS_DIR''' environment variable to the directory containing ''your'' data.

	This script will call on MATLAB to generate a CLUT, and then merge all the anatomical subdivisions generated in the previous step into two .annot files called lh.lausanne.annot and rh.lausanne.annot, respectively. These .annot files will be placed in the ${SUBJECTS_DIR}/${SUBJECT_ID}/label/ folder.		This script will call on MATLAB to generate a CLUT, and then merge all the anatomical subdivisions generated in the previous step into two .annot files called ''lh.lausanne.annot'' and ''rh.lausanne.annot'', respectively. These .annot files will be placed in the ${SUBJECTS_DIR}/${SUBJECT_ID}/label/ folder.