Preprocessfmri - Revision history

imported>Lmperry at 23:06, 6 April 2017

2017-04-06T23:06:18Z

← Older revision		Revision as of 23:06, 6 April 2017
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	# MATLAB 7.6 or later.		# MATLAB 7.6 or later.
	# Kendrick's GITHUB repository of MATLAB code (e.g. "git clone https://github.com/kendrickkay/preprocessfmri"). You will need to setup your MATLAB path accordingly. The preprocessfmri_CNI*.m files are included in this repository.		# Kendrick's GITHUB repository of MATLAB code (e.g. "git clone https://github.com/kendrickkay/preprocessfmri"). You will need to setup your MATLAB path accordingly. The preprocessfmri_CNI*.m files are included in this repository.
	# The ba_interp3 and NIFTI_20110215 MATLAB toolboxes. ~~A .zip file of each of these toolboxes is included~~ in Kendrick's ~~SVN~~ repository. ~~After doing the SVN checkout, type "unzip NIFTI_20110215.zip" and "unzip ba_interp3.zip".~~		# The ba_interp3 and NIFTI_20110215 MATLAB toolboxes. Included in Kendrick's GIT repository.
	# SPM5. I know that SPM2 will not work, but I'm not sure about other versions. You will need to setup your MATLAB path accordingly. A simple check is to type "which spm_realign". Only the portions of SPM related to motion correction are used.		# SPM5. I know that SPM2 will not work, but I'm not sure about other versions. You will need to setup your MATLAB path accordingly. A simple check is to type "which spm_realign". Only the portions of SPM related to motion correction are used.
	# FSL. Only the prelude utility of FSL is used. I have tested FSL version 4.1.6, but I'm not sure about other versions. Make sure that your shell resource file (e.g. .bashrc, .cshrc) has the appropriate FSL environment variables set, such as FSLDIR and PATH, and that the FSL configuration file is sourced. A simple check is to type "prelude" at the Unix command prompt.		# FSL. Only the prelude utility of FSL is used. I have tested FSL version 4.1.6, but I'm not sure about other versions. Make sure that your shell resource file (e.g. .bashrc, .cshrc) has the appropriate FSL environment variables set, such as FSLDIR and PATH, and that the FSL configuration file is sourced. A simple check is to type "prelude" at the Unix command prompt.

imported>Lmperry at 23:04, 6 April 2017

2017-04-06T23:04:37Z

← Older revision		Revision as of 23:04, 6 April 2017
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	# [https://github.com/kendrickkay/preprocessfmri/blob/master/preprocessfmri.m preprocessfmri.m] - This is the core code, intended to be generic and non-specific to any particular data format. You will probably not need to call this function directly. However, the function includes extensive documentation which you should probably read.		# [https://github.com/kendrickkay/preprocessfmri/blob/master/preprocessfmri.m preprocessfmri.m] - This is the core code, intended to be generic and non-specific to any particular data format. You will probably not need to call this function directly. However, the function includes extensive documentation which you should probably read.
	# [https://github.com/kendrickkay/preprocessfmri/blob/master/preprocessfmri_CNIscript.m preprocessfmri_CNIscript.m] - This is a template script file tailored for the CNI workflow. You should use this script as a starting point for processing your data. Copy and paste the script into a new file and edit as necessary.		# [https://github.com/kendrickkay/preprocessfmri/blob/master/preprocessfmri_CNIscript.m preprocessfmri_CNIscript.m] - This is a template script file tailored for the CNI workflow. You should use this script as a starting point for processing your data. Copy and paste the script into a new file and edit as necessary.
	# [https://github.com/kendrickkay/preprocessfmri/blob/master/~~preprocessfmri_CNIscript~~.m preprocessfmri_CNI.m] - This is a helper function called by preprocessfmri_CNIscript.m.		# [https://github.com/kendrickkay/preprocessfmri/blob/master/utilities/preprocessfmri_CNI.m preprocessfmri_CNI.m] - This is a helper function called by preprocessfmri_CNIscript.m.

	Once you have everything installed, have a look at preprocessfmri_CNIscript.m to see how to run the code.		Once you have everything installed, have a look at preprocessfmri_CNIscript.m to see how to run the code.

imported>Lmperry at 23:03, 6 April 2017

2017-04-06T23:03:55Z

← Older revision		Revision as of 23:03, 6 April 2017
Line 7:		Line 7:
	To use the "preprocessfmri" code, you will need the following:		To use the "preprocessfmri" code, you will need the following:
	# MATLAB 7.6 or later.		# MATLAB 7.6 or later.
	# Kendrick's ~~SVN~~ repository of MATLAB code (e.g. "~~svn checkout~~ https://~~white~~.~~stanford.edu~~/~~repos~~/~~kendrick~~"). You will need to setup your MATLAB path accordingly. The preprocessfmri_CNI*.m files are included in this repository.		# Kendrick's GITHUB repository of MATLAB code (e.g. "git clone https://github.com/kendrickkay/preprocessfmri"). You will need to setup your MATLAB path accordingly. The preprocessfmri_CNI*.m files are included in this repository.
	# The ba_interp3 and NIFTI_20110215 MATLAB toolboxes. A .zip file of each of these toolboxes is included in Kendrick's SVN repository. After doing the SVN checkout, type "unzip NIFTI_20110215.zip" and "unzip ba_interp3.zip".		# The ba_interp3 and NIFTI_20110215 MATLAB toolboxes. A .zip file of each of these toolboxes is included in Kendrick's SVN repository. After doing the SVN checkout, type "unzip NIFTI_20110215.zip" and "unzip ba_interp3.zip".
	# SPM5. I know that SPM2 will not work, but I'm not sure about other versions. You will need to setup your MATLAB path accordingly. A simple check is to type "which spm_realign". Only the portions of SPM related to motion correction are used.		# SPM5. I know that SPM2 will not work, but I'm not sure about other versions. You will need to setup your MATLAB path accordingly. A simple check is to type "which spm_realign". Only the portions of SPM related to motion correction are used.
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	"Preprocessfmri_CNI" consists of three main files		"Preprocessfmri_CNI" consists of three main files

	# [https://~~white~~.~~stanford.edu~~/~~repos~~/~~kendrick~~/preprocessfmri.m preprocessfmri.m] - This is the core code, intended to be generic and non-specific to any particular data format. You will probably not need to call this function directly. However, the function includes extensive documentation which you should probably read.		# [https://github.com/kendrickkay/preprocessfmri/blob/master/preprocessfmri.m preprocessfmri.m] - This is the core code, intended to be generic and non-specific to any particular data format. You will probably not need to call this function directly. However, the function includes extensive documentation which you should probably read.
	# [https://~~white~~.~~stanford.edu~~/~~repos~~/~~kendrick~~/preprocessfmri_CNIscript.m preprocessfmri_CNIscript.m] - This is a template script file tailored for the CNI workflow. You should use this script as a starting point for processing your data. Copy and paste the script into a new file and edit as necessary.		# [https://github.com/kendrickkay/preprocessfmri/blob/master/preprocessfmri_CNIscript.m preprocessfmri_CNIscript.m] - This is a template script file tailored for the CNI workflow. You should use this script as a starting point for processing your data. Copy and paste the script into a new file and edit as necessary.
	# [https://~~white~~.~~stanford.edu~~/~~repos~~/~~kendrick~~/~~preprocessfmri_CNI~~.m preprocessfmri_CNI.m] - This is a helper function called by preprocessfmri_CNIscript.m.		# [https://github.com/kendrickkay/preprocessfmri/blob/master/preprocessfmri_CNIscript.m preprocessfmri_CNI.m] - This is a helper function called by preprocessfmri_CNIscript.m.

	Once you have everything installed, have a look at preprocessfmri_CNIscript.m to see how to run the code.		Once you have everything installed, have a look at preprocessfmri_CNIscript.m to see how to run the code.

imported>Bobd: /* Code Overview */

2014-02-19T23:42:42Z

Code Overview

← Older revision		Revision as of 23:42, 19 February 2014
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	"Preprocessfmri_CNI" consists of three main files		"Preprocessfmri_CNI" consists of three main files

	# preprocessfmri.m - This is the core code, intended to be generic and non-specific to any particular data format. You will probably not need to call this function directly. However, the function includes extensive documentation which you should probably read.		# [https://white.stanford.edu/repos/kendrick/preprocessfmri.m preprocessfmri.m] - This is the core code, intended to be generic and non-specific to any particular data format. You will probably not need to call this function directly. However, the function includes extensive documentation which you should probably read.
	# preprocessfmri_CNIscript.m - This is a template script file tailored for the CNI workflow. You should use this script as a starting point for processing your data. Copy and paste the script into a new file and edit as necessary.		# [https://white.stanford.edu/repos/kendrick/preprocessfmri_CNIscript.m preprocessfmri_CNIscript.m] - This is a template script file tailored for the CNI workflow. You should use this script as a starting point for processing your data. Copy and paste the script into a new file and edit as necessary.
	# preprocessfmri_CNI.m - This is a helper function called by preprocessfmri_CNIscript.m.		# [https://white.stanford.edu/repos/kendrick/preprocessfmri_CNI.m preprocessfmri_CNI.m] - This is a helper function called by preprocessfmri_CNIscript.m.

	Once you have everything installed, have a look at preprocessfmri_CNIscript.m to see how to run the code.		Once you have everything installed, have a look at preprocessfmri_CNIscript.m to see how to run the code.

imported>Bobd at 23:43, 14 February 2014

2014-02-14T23:43:12Z

← Older revision		Revision as of 23:43, 14 February 2014
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	This page describes "~~preprocessfmri~~", a set of MATLAB routines written by Kendrick Kay that implements several pre-processing steps needed to analyze EPI fMRI data. The code implements slice time correction, motion correction, and [[GE_Processing#Fieldmaps \| field map distortion]] measured during the data acquisition process~~. A sample data set is available to enable you to verify your installation and to explore the effects of these corrections~~.		This page describes "preprocessfmri_CNI", a set of MATLAB routines written by Kendrick Kay that implements several pre-processing steps needed to analyze EPI fMRI data. The code implements slice time correction, motion correction, and [[GE_Processing#Fieldmaps \| field map distortion]] measured during the data acquisition process.

	Suggestions: Perhaps the code could be separated out into its different components, and these could be explained here.		Suggestions: Perhaps the code could be separated out into its different components, and these could be explained here.
Line 7:		Line 7:
	To use the "preprocessfmri" code, you will need the following:		To use the "preprocessfmri" code, you will need the following:
	# MATLAB 7.6 or later.		# MATLAB 7.6 or later.
	# Kendrick's SVN repository of MATLAB code (e.g. "svn checkout https://white.stanford.edu/repos/kendrick"). You will need to setup your MATLAB path accordingly. The ~~preprocessfmri~~*.m files are included in this repository.		# Kendrick's SVN repository of MATLAB code (e.g. "svn checkout https://white.stanford.edu/repos/kendrick"). You will need to setup your MATLAB path accordingly. The preprocessfmri_CNI*.m files are included in this repository.
	# The ba_interp3 and NIFTI_20110215 MATLAB toolboxes. A .zip file of each of these toolboxes is included in Kendrick's SVN repository. After doing the SVN checkout, type "unzip NIFTI_20110215.zip" and "unzip ba_interp3.zip".		# The ba_interp3 and NIFTI_20110215 MATLAB toolboxes. A .zip file of each of these toolboxes is included in Kendrick's SVN repository. After doing the SVN checkout, type "unzip NIFTI_20110215.zip" and "unzip ba_interp3.zip".
	# Atsushi's spirec executable, compiled for your platform (contact Kendrick for details). You will need to put the executable on your PATH, and you may need to install the fftw2 library (e.g. sudo yum install fftw2). A simple check is to type "spirec" at the Unix command prompt.
	# SPM5. I know that SPM2 will not work, but I'm not sure about other versions. You will need to setup your MATLAB path accordingly. A simple check is to type "which spm_realign". Only the portions of SPM related to motion correction are used.		# SPM5. I know that SPM2 will not work, but I'm not sure about other versions. You will need to setup your MATLAB path accordingly. A simple check is to type "which spm_realign". Only the portions of SPM related to motion correction are used.
	# FSL. Only the prelude utility of FSL is used. I have tested FSL version 4.1.6, but I'm not sure about other versions. Make sure that your shell resource file (e.g. .bashrc, .cshrc) has the appropriate FSL environment variables set, such as FSLDIR and PATH, and that the FSL configuration file is sourced. A simple check is to type "prelude" at the Unix command prompt.		# FSL. Only the prelude utility of FSL is used. I have tested FSL version 4.1.6, but I'm not sure about other versions. Make sure that your shell resource file (e.g. .bashrc, .cshrc) has the appropriate FSL environment variables set, such as FSLDIR and PATH, and that the FSL configuration file is sourced. A simple check is to type "prelude" at the Unix command prompt.
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	= Code Overview =		= Code Overview =

	"~~Preprocessfmri~~" consists of three main files		"Preprocessfmri_CNI" consists of three main files

	# preprocessfmri.m - This is the core code, intended to be generic and non-specific to any particular data format. You will probably not need to call this function directly. However, the function includes extensive documentation which you should probably read.		# preprocessfmri.m - This is the core code, intended to be generic and non-specific to any particular data format. You will probably not need to call this function directly. However, the function includes extensive documentation which you should probably read.
	# ~~preprocessfmri_standardscript~~.m - This is a template script file tailored for the CNI workflow. You should use this script as a starting point for processing your data. Copy and paste the script into a new file and edit as necessary.		# preprocessfmri_CNIscript.m - This is a template script file tailored for the CNI workflow. You should use this script as a starting point for processing your data. Copy and paste the script into a new file and edit as necessary.
	# ~~preprocessfmri_standard~~.m - This is a helper function called by ~~preprocessfmri_standardscript~~.m.		# preprocessfmri_CNI.m - This is a helper function called by preprocessfmri_CNIscript.m.

	~~= Sample dataset =~~		Once you have everything installed, have a look at preprocessfmri_CNIscript.m to see how to run the code.

	~~To verify that your code setup is correct~~, ~~try analyzing the sample dataset provided~~ at ~~[[File:PHANTOM1~~.~~tgz]]. This sample dataset consists of several DICOM directories, two raw spiral fieldmap files (P?????.7), and an analysis script.~~

	~~After unzipping the file, start up MATLAB, change~~ to ~~the directory containing the data, and then~~ run the ~~"preprocessfmri_phantom1" script. The results of the script should more or less match the sample results provided at [[File:PHANTOM1results.tgz ]]~~.

imported>Skreibig at 18:45, 23 April 2011

2011-04-23T18:45:05Z

← Older revision		Revision as of 18:45, 23 April 2011
Line 1:		Line 1:
	This page describes "preprocessfmri", a set of MATLAB routines written by Kendrick Kay that implements several pre-processing steps needed to analyze EPI fMRI data. The code implements slice time correction, motion correction, and [[GE_Processing#Fieldmaps \| field map distortion]] measured during the data acquisition process. A sample data set is available to enable you ~~can~~ to verify your installation and to explore the effects of these corrections.		This page describes "preprocessfmri", a set of MATLAB routines written by Kendrick Kay that implements several pre-processing steps needed to analyze EPI fMRI data. The code implements slice time correction, motion correction, and [[GE_Processing#Fieldmaps \| field map distortion]] measured during the data acquisition process. A sample data set is available to enable you to verify your installation and to explore the effects of these corrections.

	Suggestions: Perhaps the code could be separated out into its different components, and these could be explained here.		Suggestions: Perhaps the code could be separated out into its different components, and these could be explained here.

imported>Wandell at 03:56, 8 April 2011

2011-04-08T03:56:47Z

← Older revision		Revision as of 03:56, 8 April 2011
Line 1:		Line 1:
	This page describes "preprocessfmri", a set of MATLAB routines written by Kendrick Kay that implements several pre-processing steps needed to analyze EPI fMRI data. The code implements slice time correction, motion correction, and [[GE_Processing#Fieldmaps \| field map distortion]] measured during the data acquisition process. A sample data set is available to enable you can to verify your installation and to explore the effects of these corrections.		This page describes "preprocessfmri", a set of MATLAB routines written by Kendrick Kay that implements several pre-processing steps needed to analyze EPI fMRI data. The code implements slice time correction, motion correction, and [[GE_Processing#Fieldmaps \| field map distortion]] measured during the data acquisition process. A sample data set is available to enable you can to verify your installation and to explore the effects of these corrections.

	~~TODO~~: Perhaps the code could be separated out into its different components, and these could be explained here.		Suggestions: Perhaps the code could be separated out into its different components, and these could be explained here.


	= Requirements =		= Requirements =

imported>Wandell: /* Sample dataset */

2011-04-08T03:55:48Z

Sample dataset

← Older revision		Revision as of 03:55, 8 April 2011
Line 24:		Line 24:
	= Sample dataset =		= Sample dataset =

	To verify that your code setup is correct, try analyzing the sample dataset provided at [[File:PHANTOM1.tgz ~~Phantom1~~]]. This sample dataset consists of several DICOM directories, two raw spiral fieldmap files (P?????.7), and an analysis script.		To verify that your code setup is correct, try analyzing the sample dataset provided at [[File:PHANTOM1.tgz]]. This sample dataset consists of several DICOM directories, two raw spiral fieldmap files (P?????.7), and an analysis script.

	After unzipping the file, start up MATLAB, change to the directory containing the data, and then run the "preprocessfmri_phantom1" script. The results of the script should more or less match the sample results provided at [[File:PHANTOM1results.tgz ]].		After unzipping the file, start up MATLAB, change to the directory containing the data, and then run the "preprocessfmri_phantom1" script. The results of the script should more or less match the sample results provided at [[File:PHANTOM1results.tgz ]].

imported>Wandell: /* Sample dataset */

2011-04-08T03:55:40Z

Sample dataset

← Older revision		Revision as of 03:55, 8 April 2011
Line 24:		Line 24:
	= Sample dataset =		= Sample dataset =

	To verify that your code setup is correct, try analyzing the sample dataset provided at [[File:PHANTOM1.tgz \| Phantom1]]. This sample dataset consists of several DICOM directories, two raw spiral fieldmap files (P?????.7), and an analysis script.		To verify that your code setup is correct, try analyzing the sample dataset provided at [[File:PHANTOM1.tgz Phantom1]]. This sample dataset consists of several DICOM directories, two raw spiral fieldmap files (P?????.7), and an analysis script.

	After unzipping the file, start up MATLAB, change to the directory containing the data, and then run the "preprocessfmri_phantom1" script. The results of the script should more or less match the sample results provided at [[~~Phantom1 results \|~~ File:PHANTOM1results.tgz ]].		After unzipping the file, start up MATLAB, change to the directory containing the data, and then run the "preprocessfmri_phantom1" script. The results of the script should more or less match the sample results provided at [[File:PHANTOM1results.tgz ]].

imported>Wandell: /* Sample dataset */

2011-04-08T03:55:20Z

Sample dataset

← Older revision		Revision as of 03:55, 8 April 2011
Line 26:		Line 26:
	To verify that your code setup is correct, try analyzing the sample dataset provided at [[File:PHANTOM1.tgz \| Phantom1]]. This sample dataset consists of several DICOM directories, two raw spiral fieldmap files (P?????.7), and an analysis script.		To verify that your code setup is correct, try analyzing the sample dataset provided at [[File:PHANTOM1.tgz \| Phantom1]]. This sample dataset consists of several DICOM directories, two raw spiral fieldmap files (P?????.7), and an analysis script.

	After unzipping the file, start up MATLAB, change to the directory containing the data, and then run the "preprocessfmri_phantom1" script. The results of the script should more or less match the sample results provided at [[File:PHANTOM1results.tgz ~~\| Phantom1 results~~]].		After unzipping the file, start up MATLAB, change to the directory containing the data, and then run the "preprocessfmri_phantom1" script. The results of the script should more or less match the sample results provided at [[Phantom1 results \| File:PHANTOM1results.tgz ]].