General data processing notes - Revision history

imported>Bobd at 20:25, 13 August 2012

2012-08-13T20:25:07Z

← Older revision		Revision as of 20:25, 13 August 2012
Line 49:		Line 49:
	===Run the FSL FEAT analysis===		===Run the FSL FEAT analysis===

	fsl, feat, etc (see my slides)		fsl, feat, etc (see [https://talks.stanford.edu/cni-tutorials/ my slides] from the fMRI tutorial.)

	===Overlay on the cortical surface===		===Overlay on the cortical surface===

imported>Bobd: /* Run FreeSurfer */

2012-07-23T00:43:56Z

Run FreeSurfer

← Older revision		Revision as of 00:43, 23 July 2012
Line 45:		Line 45:
	Be sure to check your surface to make sure the segmentation is good:		Be sure to check your surface to make sure the segmentation is good:

	freeview -v ~~/scratch/fMRI/danielle/s02/~~t1.nii.gz -f /~~scratch/anatomy/multitask_s02~~/surf/lh.pial -f /~~scratch/anatomy/multitask_s02~~/surf/rh.pial		freeview -v t1.nii.gz -f ${SUBJECTS_DIR}/[subject_id]/surf/lh.pial -f ${SUBJECTS_DIR}/[subject_id]/surf/rh.pial

	===Run the FSL FEAT analysis===		===Run the FSL FEAT analysis===

imported>Bobd at 23:04, 11 July 2012

2012-07-11T23:04:39Z

← Older revision		Revision as of 23:04, 11 July 2012
Line 73:		Line 73:
	freeview -v t1.nii.gz -f ${SUBJECTS_DIR}/[subject_id]/surf/lh.inflated:overlay=[fmri.feat]/reg_surf-lh-rd/stats/zstat1.mgh -f ${SUBJECTS_DIR}/[subject_id]/surf/rh.inflated:overlay=[fmri.feat]/reg_surf-rh-rd/stats/zstat1.mgh		freeview -v t1.nii.gz -f ${SUBJECTS_DIR}/[subject_id]/surf/lh.inflated:overlay=[fmri.feat]/reg_surf-lh-rd/stats/zstat1.mgh -f ${SUBJECTS_DIR}/[subject_id]/surf/rh.inflated:overlay=[fmri.feat]/reg_surf-rh-rd/stats/zstat1.mgh

	replace [fmri.feat] with the fsl feat directory for this subject, and [subject_id] with the correct subject id.		replace [fmri.feat] with the fsl feat directory for this subject, and [subject_id] with the correct subject id. (For help in using freeview, try the [http://surfer.nmr.mgh.harvard.edu/fswiki/ToolsTutorial freesurfer tutorials].

	Or use the older viewer "tksurfer": tksurfer [subject_id] [lh\|rh] [inflated\|pial] -overlay [fmri.feat]/reg_surf-[lh\|rh]-[subject_id]/stats/zstat1.mgh		Or use the older viewer "tksurfer": tksurfer [subject_id] [lh\|rh] [inflated\|pial] -overlay [fmri.feat]/reg_surf-[lh\|rh]-[subject_id]/stats/zstat1.mgh

imported>Bobd: /* Overlay on the cortical surface */

2012-07-11T18:04:42Z

Overlay on the cortical surface

← Older revision		Revision as of 18:04, 11 July 2012
Line 71:		Line 71:
	To view the data on the native inflated or pial surface (lh for left hemisphere, rh for right):		To view the data on the native inflated or pial surface (lh for left hemisphere, rh for right):

	freeview -v t1.nii.gz -f ${~~FREESURFER~~}/[subject_id]/surf/lh.inflated:overlay=[fmri.feat]/reg_surf-lh-rd/stats/zstat1.mgh -f ${~~FREESURFER~~}/[subject_id]/surf/rh.inflated:overlay=[fmri.feat]/reg_surf-rh-rd/stats/zstat1.mgh		freeview -v t1.nii.gz -f ${SUBJECTS_DIR}/[subject_id]/surf/lh.inflated:overlay=[fmri.feat]/reg_surf-lh-rd/stats/zstat1.mgh -f ${SUBJECTS_DIR}/[subject_id]/surf/rh.inflated:overlay=[fmri.feat]/reg_surf-rh-rd/stats/zstat1.mgh

	replace [fmri.feat] with the fsl feat directory for this subject.		replace [fmri.feat] with the fsl feat directory for this subject, and [subject_id] with the correct subject id.

	Or use the older viewer "tksurfer": tksurfer [subject_id] [lh\|rh] [inflated\|pial] -overlay [fmri.feat]/reg_surf-[lh\|rh]-[subject_id]/stats/zstat1.mgh		Or use the older viewer "tksurfer": tksurfer [subject_id] [lh\|rh] [inflated\|pial] -overlay [fmri.feat]/reg_surf-[lh\|rh]-[subject_id]/stats/zstat1.mgh

imported>Bobd: /* Overlay on the cortical surface */

2012-07-11T18:03:42Z

Overlay on the cortical surface

← Older revision		Revision as of 18:03, 11 July 2012
Line 59:		Line 59:
	Be sure to replace [fmri.feat] with the directory containing the FEAT output for the analysis of this subject's fMRI data, and [subject_id] with the same id that you used in the recon-all step above.		Be sure to replace [fmri.feat] with the directory containing the FEAT output for the analysis of this subject's fMRI data, and [subject_id] with the same id that you used in the recon-all step above.

	To overlay the zmap onto the volume to check the registration~~, use~~:		Optional: overlay the zmap onto the volume to check the registration:

	tkmedit [subject_id] orig.mgz lh.white -overlay ./run1.feat/stats/zstat1.nii.gz \		tkmedit [subject_id] orig.mgz lh.white -overlay ./run1.feat/stats/zstat1.nii.gz \
Line 71:		Line 71:
	To view the data on the native inflated or pial surface (lh for left hemisphere, rh for right):		To view the data on the native inflated or pial surface (lh for left hemisphere, rh for right):

	~~tksurfer~~ [subject_id] [lh~~\|rh] [~~inflated~~\|pial] -~~overlay [fmri.feat]/reg_surf-[lh~~\|rh]~~-[subject_id]/stats/zstat1.mgh		freeview -v t1.nii.gz -f ${FREESURFER}/[subject_id]/surf/lh.inflated:overlay=[fmri.feat]/reg_surf-lh-rd/stats/zstat1.mgh -f ${FREESURFER}/[subject_id]/surf/rh.inflated:overlay=[fmri.feat]/reg_surf-rh-rd/stats/zstat1.mgh

	replace [fmri.feat] with the fsl feat directory for this subject.		replace [fmri.feat] with the fsl feat directory for this subject.

	~~Even better,~~ use ~~freeview~~:		Or use the older viewer "tksurfer": tksurfer [subject_id] [lh\|rh] [inflated\|pial] -overlay [fmri.feat]/reg_surf-[lh\|rh]-[subject_id]/stats/zstat1.mgh

	~~freeview -v /scratch/anatomy/rd/t1.nii.gz -f /scratch/anatomy/rd/surf/~~lh.inflated:overlay~~=rest2mm~~.~~ica~~/reg_surf-lh~~-rd/stats/melodic_IC.mgh -f /scratch/anatomy/rd/surf/rh.inflated:overlay=rest2mm.ica/reg_surf-~~rh-rd/stats/~~melodic_IC~~.mgh

	=Lab Equipment Notes=		=Lab Equipment Notes=

imported>Bobd: /* Overlay on the cortical surface */

2012-06-28T21:14:14Z

Overlay on the cortical surface

← Older revision		Revision as of 21:14, 28 June 2012
Line 59:		Line 59:
	Be sure to replace [fmri.feat] with the directory containing the FEAT output for the analysis of this subject's fMRI data, and [subject_id] with the same id that you used in the recon-all step above.		Be sure to replace [fmri.feat] with the directory containing the FEAT output for the analysis of this subject's fMRI data, and [subject_id] with the same id that you used in the recon-all step above.

			To overlay the zmap onto the volume to check the registration, use:
	To overlay zmap onto the volume:

	tkmedit [subject_id] orig.mgz lh.white -overlay ./run1.feat/stats/zstat1.nii.gz \		tkmedit [subject_id] orig.mgz lh.white -overlay ./run1.feat/stats/zstat1.nii.gz \

imported>Bobd: /* Run FreeSurfer */

2012-06-28T17:08:08Z

Run FreeSurfer

← Older revision		Revision as of 17:08, 28 June 2012
Line 42:		Line 42:

	recon-all -use-gpu -i t1.nii.gz -subjid [subject_id] -all		recon-all -use-gpu -i t1.nii.gz -subjid [subject_id] -all

			Be sure to check your surface to make sure the segmentation is good:

			freeview -v /scratch/fMRI/danielle/s02/t1.nii.gz -f /scratch/anatomy/multitask_s02/surf/lh.pial -f /scratch/anatomy/multitask_s02/surf/rh.pial

	===Run the FSL FEAT analysis===		===Run the FSL FEAT analysis===

imported>Bobd: /* Overlay on the cortical surface */

2012-06-28T17:06:55Z

Overlay on the cortical surface

← Older revision		Revision as of 17:06, 28 June 2012
Line 74:		Line 74:
	Even better, use freeview:		Even better, use freeview:

	freeview -v /scratch/anatomy/rd/t1.nii.gz -f /scratch/anatomy/rd/surf/lh.inflated:overlay=rest2mm.ica/reg_surf-lh-rd/stats/melodic_IC.mgh -f /scratch/anatomy/rd/surf/rh.inflated:overlay=rest2mm.ica/reg_surf-rh-rd/stats/melodic_IC.mgh		freeview -v /scratch/anatomy/rd/t1.nii.gz -f /scratch/anatomy/rd/surf/lh.inflated:overlay=rest2mm.ica/reg_surf-lh-rd/stats/melodic_IC.mgh -f /scratch/anatomy/rd/surf/rh.inflated:overlay=rest2mm.ica/reg_surf-rh-rd/stats/melodic_IC.mgh

	=Lab Equipment Notes=		=Lab Equipment Notes=

imported>Bobd: /* Run FreeSurfer */

2012-06-08T17:36:05Z

Run FreeSurfer

← Older revision		Revision as of 17:36, 8 June 2012
Line 24:		Line 24:
	export FREESURFER_HOME=/Applications/freesurfer		export FREESURFER_HOME=/Applications/freesurfer
	source $FREESURFER_HOME/SetUpFreeSurfer.sh		source $FREESURFER_HOME/SetUpFreeSurfer.sh
			export SUBJECTS_DIR=/Applications/freesurfer/subjects

	On Linux, you will run something like:		On Linux, you will run something like:
Line 29:		Line 30:
	export SUBJECTS_DIR=/scratch/anatomy		export SUBJECTS_DIR=/scratch/anatomy
	. ${FREESURFER_HOME}/SetUpFreeSurfer.sh		. ${FREESURFER_HOME}/SetUpFreeSurfer.sh
			export SUBJECTS_DIR=/scratch/anatomy

	Or better yet, put that into your .bashrc file so that it's run every time you log in.		Or better yet, put that into your .bashrc file so that it's run every time you log in.

			Be sure to set the /Applications/freesurfer/subjects to a directory with a lot of free storage space. You will need to set this enviroment variable each time you want to do something with freesurfer. Or, you can put it into your .bashrc file to have it set automatically each time you open a terminal. Also, you need to replace [t1.nii.gz] with the actual path and filename of this subject's high-res T1-weighted scan and [subject_id] with a code or name that you will use to refer to this subject (e.g., s1)

	Generate a cortical surface (and a bunch of other useful stuff) with the following commands. WARNING: this will take about 12 hours to run!		Generate a cortical surface (and a bunch of other useful stuff) with the following commands. WARNING: this will take about 12 hours to run!
			recon-all -i t1.nii.gz -subjid [subject_id] -all

	~~export SUBJECTS_DIR=/Applications/freesurfer/subjects~~		Or, if you have Cuda-capable GPU:
	~~recon~~-~~all -i [t1.nii.gz] -subjid [subject_id] -all~~

	Be sure to set the /Applications/freesurfer/subjects to a directory with a lot of free storage space. You will need to set this enviroment variable each time you want to do something with freesurfer. Or, you can put it into your .bashrc file to have it set automatically each time you open a terminal. Also, you need to replace [t1.nii.gz~~] with the actual path and filename of this subject's high-res T1~~-~~weighted scan and~~ [subject_id] ~~with a code or name that you will use to refer to this subject (e.g., s1)~~		recon-all -use-gpu -i t1.nii.gz -subjid [subject_id] -all

	===Run the FSL FEAT analysis===		===Run the FSL FEAT analysis===

			fsl, feat, etc (see my slides)

	===Overlay on the cortical surface===		===Overlay on the cortical surface===

imported>Bobd: /* Run FreeSurfer */

2012-06-08T17:12:15Z

Run FreeSurfer

← Older revision		Revision as of 17:12, 8 June 2012
Line 21:		Line 21:
	=Run FreeSurfer=		=Run FreeSurfer=

	Once you have freesurfer installed, run this to get it configured:		Once you have freesurfer installed, run something like this to get it configured on a Mac:

	export FREESURFER_HOME=/Applications/freesurfer		export FREESURFER_HOME=/Applications/freesurfer
	source $FREESURFER_HOME/SetUpFreeSurfer.sh		source $FREESURFER_HOME/SetUpFreeSurfer.sh

			On Linux, you will run something like:
			export FREESURFER_HOME=/usr/local/freesurfer
			export SUBJECTS_DIR=/scratch/anatomy
			. ${FREESURFER_HOME}/SetUpFreeSurfer.sh

			Or better yet, put that into your .bashrc file so that it's run every time you log in.

	Generate a cortical surface (and a bunch of other useful stuff) with the following commands. WARNING: this will take about 12 hours to run!		Generate a cortical surface (and a bunch of other useful stuff) with the following commands. WARNING: this will take about 12 hours to run!