Autorecon1 - Revision history

Chris: /* Stage 1b. Brain Mask Editing */

2020-09-28T15:13:50Z

Stage 1b. Brain Mask Editing

← Older revision		Revision as of 11:13, 28 September 2020
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	You would check the success of this step by overlaying the brainmask on the T1 (anatomical) image in a program called '''tkmedit'''. The masked-out voxels (i.e., the ones you want to exclude) appear as black in the mask, and the background T1 voxels remain visible. If the skull-stripping is successful, you should not see any of the background skull in the overlay because these voxels will be covered-over with black. In the (likely) event that some non-brain voxels made it through, you will use tkmedit to modify the brainmask image so that these stray non-brain voxels are excluded. Unfortunately, you have to first complete the autorecon2 step to generate the surfaces in order to overlay them. Thus, this step might properly be labeled step 2b.		You would check the success of this step by overlaying the brainmask on the T1 (anatomical) image in a program called '''tkmedit'''. The masked-out voxels (i.e., the ones you want to exclude) appear as black in the mask, and the background T1 voxels remain visible. If the skull-stripping is successful, you should not see any of the background skull in the overlay because these voxels will be covered-over with black. In the (likely) event that some non-brain voxels made it through, you will use tkmedit to modify the brainmask image so that these stray non-brain voxels are excluded. Unfortunately, you have to first complete the autorecon2 step to generate the surfaces in order to overlay them. Thus, this step might properly be labeled step 2b.

	tkmedit FS_T1_501 brainmask.mgz -aux T1.mgz -surfs		=== If you have only completed autorecon1: ===
			tkmedit FS_T1_501 brainmask.mgz -aux T1.mgz


			=== If you have already completed autorecon2: ===
			tkmedit FS_T1_501 brainmask.mgz -aux T1.mgz <span style="color:red">-surfs</span>

	A description/tutorial on brain mask editing in tkmedit can be found [https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_tktools here].		A description/tutorial on brain mask editing in tkmedit can be found [https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix_tktools here].

Chris at 14:05, 27 May 2020

2020-05-27T14:05:33Z

← Older revision		Revision as of 10:05, 27 May 2020
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	The first step in Freesurfer data processing is brain segmentation and skull-stripping.		The first step in Freesurfer data processing is brain segmentation and skull-stripping. Remember, if you already know that this will complete without errors for your dataset, you can use the -all flag, instead of the -autorecon1 flag, to complete all the autorecon steps without pausing in-between.
	== Stage 1a: Skull Stripping ==		== Stage 1a: Skull Stripping ==
	Calling <code>recon-all</code> with the -autorecon1 flag performs a number of steps related to segmenting the anatomical MRI image into brain/non-brain voxels. A shell script called <code>autorecon1.sh</code> can be found on the ubfs Scripts/Shell folder. This script simply acts as a wrapper (i.e., a convenient shortcut for executing computer code that might have a bunch of parameters that are error-prone or annoying to have to specify). You can copy this script to your ~/bin directory to be able to run it yourself:		Calling <code>recon-all</code> with the -autorecon1 flag performs a number of steps related to segmenting the anatomical MRI image into brain/non-brain voxels. A shell script called <code>autorecon1.sh</code> can be found on the ubfs Scripts/Shell folder. This script simply acts as a wrapper (i.e., a convenient shortcut for executing computer code that might have a bunch of parameters that are error-prone or annoying to have to specify). You can copy this script to your ~/bin directory to be able to run it yourself:

Cary at 16:21, 23 June 2019

2019-06-23T16:21:24Z

← Older revision		Revision as of 12:21, 23 June 2019
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	PROJECTROOT=/home/.../.../ #Change this: where are your data located?		PROJECTROOT=/home/.../.../ #Change this: where are your data located?
	SUBJECTS_DIR=${PROJECTROOT} #now tell freesurfer where the subject in question resides		SUBJECTS_DIR=${PROJECTROOT} #now tell freesurfer where the subject in question resides

	ls -1 -d */ \| sed "s,/$,," > subjects		ls -1 -d */ \| sed "s,/$,," > subjects

	for SubjectName in `cat subjects`; do		for SubjectName in `cat subjects`; do
	recon-all -autorecon1 -autorecon2 \ #replace autorecon1/autorecon2/autorecon3 with desired recons		recon-all -autorecon1 -autorecon2 \ #replace autorecon1/autorecon2/autorecon3 with desired recons

Cary at 16:20, 23 June 2019

2019-06-23T16:20:57Z

@@ Line 36: / Line 36: @@
 If you're running multiple subjects, you may want to send your output text to separate logs, e.g.:
   nohup autorecon1.sh 501 T1_ > 501_T1.out &
 == Running multiple MPRAGE files ==

Chris: /* SPM Segmentation */

2018-05-16T19:18:36Z

SPM Segmentation

← Older revision		Revision as of 15:18, 16 May 2018
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	mri_convert 001.mgz 001.nii #Convert .mgz file to .nii so SPM can read it		mri_convert 001.mgz 001.nii #Convert .mgz file to .nii so SPM can read it

	Next, if you don't already, you will need a copy of the mri_fix_script.m script in your fix directory. You can find this file ubfs/Scripts/Matlab. Once you have a copy of it, open it up in MATLAB to modify it to match your particular files:		Next, if you don't already, you will need a copy of the mri_fix_script.m script in your fix directory. You can find this file ubfs/Scripts/Matlab.

			Edit: LIES! Script is not there. Also the one I am using here has a bug. There must be multiple versions.

			Once you have a copy of it, open it up in MATLAB to modify it to match your particular files:
	First, modify line 161 to match the location of your fix directory:		First, modify line 161 to match the location of your fix directory:
	CCN.root_dir = '/home/chris/fix';		CCN.root_dir = '/home/chris/fix';

128.205.173.202: /* Mask Conversion */

2018-02-07T17:20:02Z

Mask Conversion

← Older revision		Revision as of 13:20, 7 February 2018
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	Save your modified brainmask ('''File>Save as NIfTI...''').		Save your modified brainmask ('''File>Save as NIfTI...''').

	====Mask Conversion====		====Mask Conversion and Copying====
	We need to convert our modified brainmask.nii file back to .mgz format, once again using mri_convert		We need to convert our modified brainmask.nii file back to .mgz format, once again using mri_convert
	rm brainmask.mgz #delete the unmodified .mgz file		rm brainmask.mgz #delete the unmodified .mgz file

128.205.173.202: /* Mask Application in MRICron */

2018-02-07T17:18:15Z

Mask Application in MRICron

← Older revision		Revision as of 13:18, 7 February 2018
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	cp $SUBJECTS_DIR/$SUBJID/mri/brainmask.mgz ~/fix/$SUBJID/orig		cp $SUBJECTS_DIR/$SUBJID/mri/brainmask.mgz ~/fix/$SUBJID/orig
	Launch MRICron. From the ''File'' menu, load the brainmask.mgz file. Next, from the '''Draw''' menu, select '''Open VOI...''', and find the GMWM.nii mask file (the file won't be visible in the window until you change the file format filter from '''Volume of interest (*.voi)''' to '''Neuroimaging'''.		Launch MRICron. From the ''File'' menu, load the brainmask.mgz file. Next, from the '''Draw''' menu, select '''Open VOI...''', and find the GMWM.nii mask file (the file won't be visible in the window until you change the file format filter from '''Volume of interest (*.voi)''' to '''Neuroimaging'''.
	You should now see the voxels included in your mask with a red overlay. Finally, we can delete the nonsense voxels ~~from the ''Draw'' menu~~ by '''Mask image with VOI > Preserve regions within VOI'''.		You should now see the voxels included in your mask with a red overlay. Finally, we can delete the nonsense voxels by selecting '''Draw>Mask image with VOI > Preserve regions within VOI'''.
	Save your modified brainmask ('''File>Save as NIfTI...''').		Save your modified brainmask ('''File>Save as NIfTI...''').

128.205.173.202: /* Mask Application in MRICron */

2018-02-07T17:17:32Z

Mask Application in MRICron

← Older revision		Revision as of 13:17, 7 February 2018
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	We will now apply our mask to the brainmask.mgz file generated by recon-all. Copy brainmask.mgz from the FreeSurfer $SUBJID/mri/brainmask.mgz to your fix/$SUBJID/orig directory.		We will now apply our mask to the brainmask.mgz file generated by recon-all. Copy brainmask.mgz from the FreeSurfer $SUBJID/mri/brainmask.mgz to your fix/$SUBJID/orig directory.
	cp $SUBJECTS_DIR/$SUBJID/mri/brainmask.mgz ~/fix/$SUBJID/orig		cp $SUBJECTS_DIR/$SUBJID/mri/brainmask.mgz ~/fix/$SUBJID/orig
	Launch MRICron. From the ''File'' menu, load the brainmask.mgz file. Next, from the ''Draw'' menu, select ''Open VOI...'', and find the GMWM.nii mask file (the file won't be visible in the window until you change the file format filter from '''Volume of interest (*.voi)''' to '''Neuroimaging'''.		Launch MRICron. From the ''File'' menu, load the brainmask.mgz file. Next, from the '''Draw''' menu, select '''Open VOI...''', and find the GMWM.nii mask file (the file won't be visible in the window until you change the file format filter from '''Volume of interest (*.voi)''' to '''Neuroimaging'''.
	You should now see the voxels included in your mask with a red overlay. Finally, we can delete the nonsense voxels from the ''Draw'' menu by '''Mask image with VOI > Preserve regions within VOI'''.		You should now see the voxels included in your mask with a red overlay. Finally, we can delete the nonsense voxels from the ''Draw'' menu by '''Mask image with VOI > Preserve regions within VOI'''.
	Save your modified brainmask ('''File>Save as ~~nii~~''').		Save your modified brainmask ('''File>Save as NIfTI...''').

	====Mask Conversion====		====Mask Conversion====

128.205.173.202: /* Mask Application in MRICron */

2018-02-07T17:16:24Z

Mask Application in MRICron

← Older revision		Revision as of 13:16, 7 February 2018
Line 126:		Line 126:
	Launch MRICron. From the ''File'' menu, load the brainmask.mgz file. Next, from the ''Draw'' menu, select ''Open VOI...'', and find the GMWM.nii mask file (the file won't be visible in the window until you change the file format filter from '''Volume of interest (*.voi)''' to '''Neuroimaging'''.		Launch MRICron. From the ''File'' menu, load the brainmask.mgz file. Next, from the ''Draw'' menu, select ''Open VOI...'', and find the GMWM.nii mask file (the file won't be visible in the window until you change the file format filter from '''Volume of interest (*.voi)''' to '''Neuroimaging'''.
	You should now see the voxels included in your mask with a red overlay. Finally, we can delete the nonsense voxels from the ''Draw'' menu by '''Mask image with VOI > Preserve regions within VOI'''.		You should now see the voxels included in your mask with a red overlay. Finally, we can delete the nonsense voxels from the ''Draw'' menu by '''Mask image with VOI > Preserve regions within VOI'''.
	Save your modified brainmask.mgz. Finally, copy the modified file to the FreeSurfer subject directory, overwriting the original (you might first make a backup copy of the original brainmask.mgz if you want to play it safe).		Save your modified brainmask ('''File>Save as nii''').

			====Mask Conversion====
			We need to convert our modified brainmask.nii file back to .mgz format, once again using mri_convert
			rm brainmask.mgz #delete the unmodified .mgz file
			mri_convert brainmask.nii brainmask.mgz #convert the modified .nii file to .mgz format
			Finally, copy the modified brainmask.mgz file to the FreeSurfer subject directory, overwriting the original (you might first make a backup copy of the original brainmask.mgz if you want to play it safe).

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

128.205.173.88: /* Quick Brain Mask Editing Using SPM and MRICron */

2018-02-07T17:12:12Z

Quick Brain Mask Editing Using SPM and MRICron

← Older revision		Revision as of 13:12, 7 February 2018
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	mri_convert 001.mgz 001.nii #Convert .mgz file to .nii so SPM can read it		mri_convert 001.mgz 001.nii #Convert .mgz file to .nii so SPM can read it

	Next, if you don't already, you will need a copy of the mri_fix_script.m script ~~that you~~ can find in ubfs/Scripts/Matlab. ~~Open~~ it up in MATLAB ~~and~~ modify line 161:		Next, if you don't already, you will need a copy of the mri_fix_script.m script in your fix directory. You can find this file ubfs/Scripts/Matlab. Once you have a copy of it, open it up in MATLAB to modify it to match your particular files:
			First, modify line 161 to match the location of your fix directory:
	CCN.root_dir = '/home/chris/fix';		CCN.root_dir = '/home/chris/fix';
	Change the directory to match your own directory location. Likewise, the working directory will need to be changed (line 168)		Change the directory to match your own directory location. Likewise, the working directory will need to be changed (line 168) to the same location:
	CCN.work_dir = '/home/chris/fix';		CCN.work_dir = '/home/chris/fix';

	A couple lines down (line 171) is the list of subject IDs. Change this to match your subject folder names:		A couple lines down (line 171) is the list of subject IDs. Change this to match your subject folder names:
	CCN.all_subjects = {'FS_0238'};		CCN.all_subjects = {'FS_0238'};

	That should be all the changes required. This script will work on wernickesarea, brocasarea and accumbens. It is run in MATLAB, and requires everything under /opt/spm12 and /opt/northwestern to be in your path (see Chris for his copy of startup_spm12.m). If these conditions are met, you should be able to run it from your ~/fix directory:		That should be all the changes required. This script will work on wernickesarea, brocasarea and accumbens. It is run in MATLAB, and requires everything under /opt/spm12 and /opt/northwestern to be in your path (see Chris for his copy of startup_spm12.m). If these conditions are met, you should be able to run it from your ~/fix directory:
	mri_fix_script		mri_fix_script
Line 127:		Line 126:
	Launch MRICron. From the ''File'' menu, load the brainmask.mgz file. Next, from the ''Draw'' menu, select ''Open VOI...'', and find the GMWM.nii mask file (the file won't be visible in the window until you change the file format filter from '''Volume of interest (*.voi)''' to '''Neuroimaging'''.		Launch MRICron. From the ''File'' menu, load the brainmask.mgz file. Next, from the ''Draw'' menu, select ''Open VOI...'', and find the GMWM.nii mask file (the file won't be visible in the window until you change the file format filter from '''Volume of interest (*.voi)''' to '''Neuroimaging'''.
	You should now see the voxels included in your mask with a red overlay. Finally, we can delete the nonsense voxels from the ''Draw'' menu by '''Mask image with VOI > Preserve regions within VOI'''.		You should now see the voxels included in your mask with a red overlay. Finally, we can delete the nonsense voxels from the ''Draw'' menu by '''Mask image with VOI > Preserve regions within VOI'''.
	Save your modified brainmask.~~nii~~, ~~replacing~~ the original ~~file~~.		Save your modified brainmask.mgz. Finally, copy the modified file to the FreeSurfer subject directory, overwriting the original (you might first make a backup copy of the original brainmask.mgz if you want to play it safe).

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