Freesurfer Abridged - Revision history

Chris: /* Functional */

2022-05-11T16:55:54Z

Functional

← Older revision		Revision as of 12:55, 11 May 2022
Line 37:		Line 37:
	#* Semcat processing		#* Semcat processing
	#** In terminal, <code> matlab &</code>		#** In terminal, <code> matlab &</code>
	#** In matlab, <code>~~startup_smp12~~</code>		#** In matlab, <code>startup_spm12</code>
	# Check with your local Principle Investigator™ or Graduate Work Horse™ for more details about Semcat bold files**		# Check with your local Principle Investigator™ or Graduate Work Horse™ for more details about Semcat bold files**
	#* LDT processing		#* LDT processing

Rebecca: /* Functional */

2018-04-04T14:34:33Z

Functional

← Older revision		Revision as of 10:34, 4 April 2018
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	#** In terminal, <code> matlab &</code>		#** In terminal, <code> matlab &</code>
	#** In matlab, <code>startup_smp12</code>		#** In matlab, <code>startup_smp12</code>
	#**		# Check with your local Principle Investigator™ or Graduate Work Horse™ for more details about Semcat bold files**
	#* LDT processing		#* LDT processing
	#** In terminal, <code>matlab &</code>		#** In terminal, <code>matlab &</code>
	#** nii_4D_drop_vols('f.nii', [# vols to drop~~-- see #LINK>~~])		#** nii_4D_drop_vols('f.nii', [# vols to drop])
	#** set_TR(2.047, [1 2 3 4 5 6], 'f.nii')		#** set_TR(2.047, [1 2 3 4 5 6], 'f.nii')
	#** d=datenum('DD-Mmm-YYYY') (e.g. '05-Oct-1997')		#** d=datenum('DD-Mmm-YYYY') (e.g. '05-Oct-1997')
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	#** FSTSExtractor('prefix', 'LDT_', 'subject', subj_ID, 'run', i, 'tr', 2.047, 'volumes_dropped', <initial # drop vols>, 'date', d)		#** FSTSExtractor('prefix', 'LDT_', 'subject', subj_ID, 'run', i, 'tr', 2.047, 'volumes_dropped', <initial # drop vols>, 'date', d)
	#*** This step must be completed for each f.nii file in each bold folder		#*** This step must be completed for each f.nii file in each bold folder
	#*** IT IS VERY IMPORTANT to look at what volumes to drop. It will likely not be the same for each bold file, unless it is a newer LDT participant. You can find more information ~~#LINK~~ here.		#*** IT IS VERY IMPORTANT to look at what volumes to drop. It will likely not be the same for each bold file, unless it is a newer LDT participant. You can find more information [[http://ccnlab.psy.buffalo.edu/wiki/index.php/Freesurfer_BOLD_files]] here.
	# Analysis		# Analysis
	#* cd to subject folder		#* cd to subject folder

128.205.172.41: /* Functional */

2017-12-08T18:24:09Z

Functional

← Older revision		Revision as of 14:24, 8 December 2017
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	# Bold file preparation		# Bold file preparation
	#* Semcat processing		#* Semcat processing
	#** ~~Step a:~~ In terminal, <code> matlab &</code>		#** In terminal, <code> matlab &</code>
	#** ~~Step b:~~ In matlab, <code>~~startup_smp8~~</code>		#** In matlab, <code>startup_smp12</code>
	#** ~~Step c:~~		#**
	#* LDT processing		#* LDT processing
			#** In terminal, <code>matlab &</code>
			#** nii_4D_drop_vols('f.nii', [# vols to drop-- see #LINK>])
			#** set_TR(2.047, [1 2 3 4 5 6], 'f.nii')
			#** d=datenum('DD-Mmm-YYYY') (e.g. '05-Oct-1997')
			#** subj_ID='0183'
			#** FSTSExtractor('prefix', 'LDT_', 'subject', subj_ID, 'run', i, 'tr', 2.047, 'volumes_dropped', <initial # drop vols>, 'date', d)
			#*** This step must be completed for each f.nii file in each bold folder
			#*** IT IS VERY IMPORTANT to look at what volumes to drop. It will likely not be the same for each bold file, unless it is a newer LDT participant. You can find more information #LINK here.
	# Analysis		# Analysis
			#* cd to subject folder
			#* mkanalysis.sh
	# Contrasts		# Contrasts
			#* cd to subject folder
			#* Run <code>mkcontrast.sh</code>
	# Pre-processing		# Pre-processing
			#* Run <code>preproc-sess -per-run -fwhm 6 -surface self lhrh -fsd bold -s FS_<subj_ID></code>
	# Selxavg		# Selxavg
			#* Run <code>selxavg3-sess -s <subjectname> -analysis <analysis path></code>
			#* Analysis path is where your LDT.?h.sm6 folders are.
	# (Optional) Clut and Subparcellation		# (Optional) Clut and Subparcellation
			#* Run <code>clut.sh FS_<subj_ID></code>
			#* Run <code>subpar.py FS_<subj_ID></code>
	# Blobs		# Blobs

	== Timeseries Analysis ==		== Timeseries Analysis ==

128.205.172.41: /* Setting Up */

2017-12-08T17:59:34Z

Setting Up

← Older revision		Revision as of 13:59, 8 December 2017
Line 2:		Line 2:
	*Note: I am using FS_0184 (semcat) as an example; fill in the parts specific to FS_0184 with the parts specific to your subject		*Note: I am using FS_0184 (semcat) as an example; fill in the parts specific to FS_0184 with the parts specific to your subject

	This is an <i>abridged</i> version of the more detailed list provided elsewhere in the ~~wii~~		This is an <i>abridged</i> version of the more detailed list provided elsewhere in the wiki.

	== Structural ==		== Structural ==

128.205.172.41: /* Functional */

2017-11-17T18:47:54Z

Functional

← Older revision		Revision as of 14:47, 17 November 2017
Line 35:		Line 35:

	# Bold file preparation		# Bold file preparation
			#* Semcat processing
			#** Step a: In terminal, <code> matlab &</code>
			#** Step b: In matlab, <code>startup_smp8</code>
			#** Step c:
			#* LDT processing

	# Analysis		# Analysis
	# Contrasts		# Contrasts
	# Pre-processing		# Pre-processing
	# Selxavg		# Selxavg
	# ~~Sub-parcellation~~		# (Optional) Clut and Subparcellation
	# Clut
	# Blobs		# Blobs

	== Timeseries Analysis ==		== Timeseries Analysis ==

128.205.172.41: /* Structural */

2017-11-17T18:14:18Z

Structural

← Older revision		Revision as of 14:14, 17 November 2017
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	== Structural ==		== Structural ==

	*Slicer		# Slicer
	** In terminal, <code>Slicer &</code>		#* In terminal, <code>Slicer &</code>
	** Load data brainmask.nii		#* Load data brainmask.nii
	** Save data as brainmask.mgz		#* Save data as brainmask.mgz
	** Results: creates brainmask.mgz file		#* Results: creates brainmask.mgz file
	* Autorecon 1		# Autorecon 1
	** In terminal, <code>autorecon1_SC.sh FS_0184</code>		#* In terminal, <code>autorecon1_SC.sh FS_0184</code>
	** Don't bother editing after this step; skip to autorecon 2		#* Don't bother editing after this step; skip to autorecon 2
	** Result: populates mri folder (includes "T1.mgz")		#* Result: populates mri folder (includes "T1.mgz")
	* Autorecon 2		# Autorecon 2
	** In terminal, <code>autorecon2_SC.sh FS_0184</code>		#* In terminal, <code>autorecon2_SC.sh FS_0184</code>
	** Editing		#* Editing
	*** One terminal, <code>tksurfer FS_0184 lh inflated</code>		#** One terminal, <code>tksurfer FS_0184 lh inflated</code>
	*** In another terminal, <code>tkmedit FS_0184 brainmask.mgz -aux T1.mgz -surfs</code>		#** In another terminal, <code>tkmedit FS_0184 brainmask.mgz -aux T1.mgz -surfs</code>
	*** Look for any noticable spikes in the tksurfer brain and edit the brainmask (tkmedit). See wiki page for details; this is the most labor intensive part of anatomical so make sure you're doing it right.		#** Look for any noticable spikes in the tksurfer brain and edit the brainmask (tkmedit). See wiki page for details; this is the most labor intensive part of anatomical so make sure you're doing it right.
	** Results: creates lh.cortex.label and rh.cortex.label in label folder		#* Results: creates lh.cortex.label and rh.cortex.label in label folder
	* Autorecon 3		# Autorecon 3
	** In terminal, <code>autorecon3_SC.sh FS_0184</code>		#* In terminal, <code>autorecon3_SC.sh FS_0184</code>
	** Editing		#* Editing
	*** In terminal, <code>tksurfer -annot aparc FS_0184 lh pial</code>		#** In terminal, <code>tksurfer -annot aparc FS_0184 lh pial</code>
	*** If needed, reference <code>tksurfer -annot aparc fsaverage lh pial</code>		#** If needed, reference <code>tksurfer -annot aparc fsaverage lh pial</code>
	*** Repeat with right hemi		#** Repeat with right hemi
	*** Make sure to EXPORT ANNOTATION! Do not "save overlay!"		#** Make sure to EXPORT ANNOTATION! Do not "save overlay!"
	*** Again, be sure to see the autorecon3 page		#** Again, be sure to see the autorecon3 page
	**Result: populates label folder (includes "lh.aparc.annot" and "rh.aparc.annot")		#*Result: populates label folder (includes "lh.aparc.annot" and "rh.aparc.annot")

	== Functional ==		== Functional ==

128.205.172.41: /* Functional */

2017-11-17T18:12:55Z

Functional

← Older revision		Revision as of 14:12, 17 November 2017
Line 34:		Line 34:
	== Functional ==		== Functional ==

	# ~~Matlab~~		# Bold file preparation
	# Analysis		# Analysis
	# Contrasts		# Contrasts
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	# Clut		# Clut
	# Blobs		# Blobs

	== Timeseries Analysis ==		== Timeseries Analysis ==

128.205.172.41: /* Setting Up */

2017-11-17T18:03:03Z

Setting Up

← Older revision		Revision as of 14:03, 17 November 2017
Line 1:		Line 1:
	== Setting Up ==		== Setting Up ==
	*Note: I am using FS_0184 (semcat) as an example; fill in the parts specific to FS_0184 with the parts specific to your subject		*Note: I am using FS_0184 (semcat) as an example; fill in the parts specific to FS_0184 with the parts specific to your subject

			This is an <i>abridged</i> version of the more detailed list provided elsewhere in the wii

	== Structural ==		== Structural ==

128.205.172.41: /* Structural */

2017-11-17T17:59:52Z

Structural

← Older revision		Revision as of 13:59, 17 November 2017
Line 7:		Line 7:
	** Load data brainmask.nii		** Load data brainmask.nii
	** Save data as brainmask.mgz		** Save data as brainmask.mgz
	** ~~Creates~~ brainmask.mgz file		** Results: creates brainmask.mgz file
	* Autorecon 1		* Autorecon 1
	** In terminal, <code>autorecon1_SC.sh FS_0184</code>		** In terminal, <code>autorecon1_SC.sh FS_0184</code>

128.205.172.41: /* Structural */

2017-11-17T17:59:35Z

Structural

← Older revision		Revision as of 13:59, 17 November 2017
Line 7:		Line 7:
	** Load data brainmask.nii		** Load data brainmask.nii
	** Save data as brainmask.mgz		** Save data as brainmask.mgz
			** Creates brainmask.mgz file
	* Autorecon 1		* Autorecon 1
	** In terminal, <code>autorecon1_SC.sh FS_0184</code>		** In terminal, <code>autorecon1_SC.sh FS_0184</code>
	** Don't bother editing after this step; skip to autorecon 2		** Don't bother editing after this step; skip to autorecon 2
			** Result: populates mri folder (includes "T1.mgz")
	* Autorecon 2		* Autorecon 2
	** In terminal, <code>autorecon2_SC.sh FS_0184</code>		** In terminal, <code>autorecon2_SC.sh FS_0184</code>
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	*** In another terminal, <code>tkmedit FS_0184 brainmask.mgz -aux T1.mgz -surfs</code>		*** In another terminal, <code>tkmedit FS_0184 brainmask.mgz -aux T1.mgz -surfs</code>
	*** Look for any noticable spikes in the tksurfer brain and edit the brainmask (tkmedit). See wiki page for details; this is the most labor intensive part of anatomical so make sure you're doing it right.		*** Look for any noticable spikes in the tksurfer brain and edit the brainmask (tkmedit). See wiki page for details; this is the most labor intensive part of anatomical so make sure you're doing it right.
			** Results: creates lh.cortex.label and rh.cortex.label in label folder
	* Autorecon 3		* Autorecon 3
	** In terminal, <code>autorecon3_SC.sh FS_0184</code>		** In terminal, <code>autorecon3_SC.sh FS_0184</code>
	** Editing		** Editing
	***		*** In terminal, <code>tksurfer -annot aparc FS_0184 lh pial</code>
			*** If needed, reference <code>tksurfer -annot aparc fsaverage lh pial</code>
			*** Repeat with right hemi
			*** Make sure to EXPORT ANNOTATION! Do not "save overlay!"
			*** Again, be sure to see the autorecon3 page
			**Result: populates label folder (includes "lh.aparc.annot" and "rh.aparc.annot")

	== Functional ==		== Functional ==