FreeSurfer - Revision history

Chris: /* batch_autorecon.sh */

2022-06-24T17:00:29Z

batch_autorecon.sh

← Older revision		Revision as of 13:00, 24 June 2022
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	while read s; do		while read s; do
	<span style="color:green">#note that ~~the next line might need to change~~ depending on the locations and names		<span style="color:green">#note that, depending on the locations and names of your anatomical data files,
	#of your anatomical data</span>		#you might have to modify the next line to reflect those differences</span>
	recon-all -all -i ./$s/T1.nii.gz -T2 ./$s/T2.nii.gz -subjid FS_$s		recon-all -all -i ./$s/T1.nii.gz -T2 ./$s/T2.nii.gz -subjid FS_$s
	done<$1		done<$1

Chris: /* batch_autorecon.sh */

2022-06-24T16:59:06Z

batch_autorecon.sh

← Older revision		Revision as of 12:59, 24 June 2022
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	while read s; do		while read s; do
			<span style="color:green">#note that the next line might need to change depending on the locations and names
			#of your anatomical data</span>
	recon-all -all -i ./$s/T1.nii.gz -T2 ./$s/T2.nii.gz -subjid FS_$s		recon-all -all -i ./$s/T1.nii.gz -T2 ./$s/T2.nii.gz -subjid FS_$s
	done<$1		done<$1

Chris: /* Organization */

2022-06-24T16:55:54Z

Organization

← Older revision		Revision as of 12:55, 24 June 2022
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	SUBJECTS_DIR=`pwd`		SUBJECTS_DIR=`pwd`
	echo $SUBJECTS_DIR		echo $SUBJECTS_DIR
	The first line above, <code>cd ~</code> moves you to your home directory. The second line moves you to Projects folder that might contain several sets of experiments. The third line of code moves you into the subdirectory containing the LDT data. The fourth line sets the SUBJECTS_DIR environment variable to whatever gets printed out when you execute the <code>pwd</code> command (the <code>pwd</code> command '''<u>p</u>'''rints the current '''<u>w</u>'''orking '''<u>d</u>'''irectory). As a result, the current working directory becomes the new SUBJECTS_DIR after you execute this command, as you can see when you execute the last line of code. Note that in the <code>SUBJECTS_DIR=`pwd`</code> line, those are back-quotes, which you might find on your keyboard sharing a key with the ~ character. <code>`</code> is not the same character as <code>'</code>. When you enclose a command in a pair of back-quotes, you are telling the operating something along the lines of "this is a command that I want you to execute first, before using its output to figure out the rest of this business."		The first line above, <code>cd ~</code> moves you to your home directory. The second line moves you to Projects folder that might contain several sets of experiments. The third line of code moves you into the subdirectory containing the LDT data. The fourth line sets the SUBJECTS_DIR environment variable to whatever gets printed out when you execute the <code>pwd</code> command (the <code>pwd</code> command '''<u>p</u>'''rints the current '''<u>w</u>'''orking '''<u>d</u>'''irectory). As a result, the current working directory becomes the new SUBJECTS_DIR after you execute this command, as you can see when you execute the last line of code.

			Note that in the <code>SUBJECTS_DIR=`pwd`</code> line, those are '''back-quotes''', which you might find on your keyboard sharing a key with the ~ character. <code>`</code> is not the same character as <code>'</code>. When you enclose a command in a pair of back-quotes, you are telling the operating something along the lines of "this is a command that I want you to execute first, before using its output to figure out the rest of this business."

Chris: /* Anatomical Surface Mesh Construction with Recon-All */

2022-06-24T16:46:53Z

Anatomical Surface Mesh Construction with Recon-All

@@ Line 125: / Line 125: @@
   tksurfer ${subjectID} lh inflated #this will display the left hemisphere (lh) inflated surface
 Check both the lh and rh surfaces. If the brain appears lumpy or there are odd points sticking out, proceed to [[Autorecon2]] editing.
 == Functional Analysis ==

Chris: /* FS-FAST Functional Analysis */

2022-05-24T17:12:14Z

FS-FAST Functional Analysis

← Older revision		Revision as of 13:12, 24 May 2022
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	#Create (or copy if experiment used a fixed schedule) your paradigm files for each fMRI run, and edit them using matlab (see "[[Par-Files]]").		#Create (or copy if experiment used a fixed schedule) your paradigm files for each fMRI run, and edit them using matlab (see "[[Par-Files]]").
	#*When editing par files, be sure to check how many volumes to drop for each par file; it may be different every time! See above link for more details.		#*When editing par files, be sure to check how many volumes to drop for each par file; it may be different every time! See above link for more details.
	#Create a subjects text file in your $SUBJECTS_DIR called "~~subjectname~~" that contains a list of your subjects necessary for ~~later~~ (used for [[Configure preproc-sess\|preproc-sess]])		#Create a subjects text file in your $SUBJECTS_DIR called "subjects" (or some other name) that contains a list of your subjects necessary for batch processing (used for [[Configure preproc-sess\|preproc-sess]])
	#*A quick way to do this, assuming you want to preprocess everyone, is to pipe the results of the ls command with the -1 switch (1 per line) into grep and then redirect the output to a file:		#*A quick way to do this, assuming you want to preprocess everyone, is to pipe the results of the ls command with the -1 switch (1 per line) into grep and then redirect the output to a file:
	#<code>ls -1 -d FS/ \| sed "s,/$,," > subjects</code>		#<code>ls -1 -d FS/ \| sed "s,/$,," > subjects</code>
	#*This will list the names of any directories in the current director starting with "FS", and strip off the trailing forward slash		#*This will list the names of any directories in the current director starting with "FS", and strip off the trailing forward slash
			#Create a text file called <code>subjectname</code> in each of the subject folders. The file is a 1-line plaintext file that just contains the name of the subject.
	#Configure your analyses (using [[Configure mkanalysis-sess\|mkanalysis-sess]])		#Configure your analyses (using [[Configure mkanalysis-sess\|mkanalysis-sess]])
	#Configure your contrast (using [[Configure mkcontrast-sess\|mkcontrast-sess]])		#Configure your contrast (using [[Configure mkcontrast-sess\|mkcontrast-sess]])

Chris: /* Installing FastSurfer */

2022-04-06T14:26:00Z

Installing FastSurfer

← Older revision		Revision as of 10:26, 6 April 2022
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	= FastSurfer =		= FastSurfer =
	[https://deep-mi.org/research/fastsurfer/ FastSurfer] "is a fast and extensively validated deep-learning pipeline for the fully automated processing of structural human brain MRIs." It works on top of a FreeSurfer installation, requires Python 3, and can be obtained through GitHub.		[https://deep-mi.org/research/fastsurfer/ FastSurfer] "is a fast and extensively validated deep-learning pipeline for the fully automated processing of structural human brain MRIs." It works on top of a FreeSurfer installation, requires Python 3, and can be obtained through GitHub.
	== ~~Installing~~ FastSurfer ==		== Obtaining FastSurfer ==
	# Git Clone the repository at https://github.com/deep-mi/FastSurfer		# Git Clone the repository at https://github.com/deep-mi/FastSurfer
	# pip3-install -r requirements.txt		# pip3-install -r requirements.txt

Chris at 14:25, 6 April 2022

2022-04-06T14:25:22Z

← Older revision		Revision as of 10:25, 6 April 2022
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	<span style="color:red">'''If you are completely perplexed why something doesn't work out when you followed the directions to the letter, the first thing you should do is throw out your assumption that you typed in the command correctly.'''</span>		<span style="color:red">'''If you are completely perplexed why something doesn't work out when you followed the directions to the letter, the first thing you should do is throw out your assumption that you typed in the command correctly.'''</span>

			= FastSurfer =
			[https://deep-mi.org/research/fastsurfer/ FastSurfer] "is a fast and extensively validated deep-learning pipeline for the fully automated processing of structural human brain MRIs." It works on top of a FreeSurfer installation, requires Python 3, and can be obtained through GitHub.
			== Installing FastSurfer ==
			# Git Clone the repository at https://github.com/deep-mi/FastSurfer
			# pip3-install -r requirements.txt
			# There may be an issue installing LaPy with the requirements file. I overcame this by visiting github.com/Deep-MI/LaPy and installing it separately

	[[Category:FreeSurfer]]		[[Category:FreeSurfer]]

Chris: /* Is Freesurfer in your path? */

2022-02-02T22:12:08Z

Is Freesurfer in your path?

@@ Line 185: / Line 185: @@
 #It's documented elsewhere on the wiki
 #If you're confused about how to set SUBJECTS_DIR, you're also likely to just blindly type whatever example command I give without understanding what the command does. If this is the case, please become more proficient with the lab's procedures and software.
 === ERROR: Flag unrecognized. ===

Chris: /* recon-all -all */

2022-02-02T22:10:39Z

recon-all -all

← Older revision		Revision as of 18:10, 2 February 2022
Line 113:		Line 113:
	-subjid FS_${subjectID}		-subjid FS_${subjectID}

	The above command will find the <span style="color:green">T1w.nii.gz</span> file for whatever subject is stored in <span style="color:red">${subjectID}</span>, and run all processing steps. The output files will be found in the FreeSurfer subject folder called FS_<span style="color:red">${subjectID}</span>. In this case, folder ~~FS_sub~~-01 will be created in the ${SUBJECTS_DIR}. On the GPU-enabled workstations, this process should take between 6-7 hours. If your anatomical data files have a different naming convention (e.g., include session or acquisition information or have a different file extension), you will probably end up changing the <span style="color:green">code in green</span>.		The above command will find the <span style="color:green">T1w.nii.gz</span> file for whatever subject is stored in <span style="color:red">${subjectID}</span>, and run all processing steps. The output files will be found in the FreeSurfer subject folder called FS_<span style="color:red">${subjectID}</span>. In this case, folder FS_<span style="color:red">sub-01</span> will be created in the ${SUBJECTS_DIR}. On the GPU-enabled workstations, this process should take between 6-7 hours. If your anatomical data files have a different naming convention (e.g., include session or acquisition information or have a different file extension), you will probably end up changing the <span style="color:green">code in green</span>.

	=== recon-all in stages ===		=== recon-all in stages ===

Chris: /* recon-all -all */

2022-02-02T22:10:03Z

recon-all -all

← Older revision		Revision as of 18:10, 2 February 2022
Line 113:		Line 113:
	-subjid FS_${subjectID}		-subjid FS_${subjectID}

	The above command will find the <span style="color:green">T1w.nii.gz</span> file for whatever subject is stored in ${subjectID}, and run all processing steps. The output files will be found in the FreeSurfer subject folder called FS_${subjectID}. In this case, folder FS_sub-01 will be created in the ${SUBJECTS_DIR}. On the GPU-enabled workstations, this process should take between 6-7 hours. If your anatomical data files have a different naming convention (e.g., include session or acquisition information or have a different file extension), you will probably end up changing the <span style="color:green">code in green</span>.		The above command will find the <span style="color:green">T1w.nii.gz</span> file for whatever subject is stored in <span style="color:red">${subjectID}</span>, and run all processing steps. The output files will be found in the FreeSurfer subject folder called FS_<span style="color:red">${subjectID}</span>. In this case, folder FS_sub-01 will be created in the ${SUBJECTS_DIR}. On the GPU-enabled workstations, this process should take between 6-7 hours. If your anatomical data files have a different naming convention (e.g., include session or acquisition information or have a different file extension), you will probably end up changing the <span style="color:green">code in green</span>.

	=== recon-all in stages ===		=== recon-all in stages ===