Hello,
I'm getting started with freesurfer. I've played around with some of the tutorial data for fs-fast (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1) and was able to follow along and successfully carry out the preprocessing exercises (which sufficed for my purposes), which also included running register-sess on the "rest" tutorial data for sess01.
I've run into a few gotchas with some resting state data, and wanted to know if there are any problems specific to processing resting state data that can be easily avoided?
For example, here's the file structure: Project root: /home/chris/resting
Anatomical data root ($SUBJECTS_DIR): /home/chris/resting/anat
Functional data root ($FUNCTIONALS_DIR): /home/chris/resting/func
Subject 1 anatomical directory: $SUBJECTS_DIR/sub00156 (already run through recon-all)
Subject 1 functional directory: $FUNCTIONALS_DIR/sub00156 contains: subjectname ("sub00156") and a nii file in a nested subdirectory: $FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz Where f.nii.gz is some resting state data (hence no paradigm files)
For my inaugural attempt, I've run anatomical data for a participant through recon-all, and was having problems registering $FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz to the surface map in $SUBJECTS_DIR/sub00156. After some trial and error and wandering through this mailing list, I found I had to first run mktemplate-sess and then register-sess (the fs-fast tutorial lead me to believe everything was automatically handled by preproc-sess). Are these deviations a foreseeable consequence of working with resting state data? Is there some documentation of important considerations for working with resting state data?
Thanks for any help,
Chris
Hi Chris, it should have been done with preproc-sess. What was your preproc-sess command line? At some point, I had it set up so that it would go to the bold directory by default unless you used "-fsd rest". Newer versions require you to specify the FSD specifically.
doug
On 11/5/12 9:38 PM, Chris McNorgan wrote:
Hello,
I'm getting started with freesurfer. I've played around with some of the tutorial data for fs-fast (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1) and was able to follow along and successfully carry out the preprocessing exercises (which sufficed for my purposes), which also included running register-sess on the "rest" tutorial data for sess01.
I've run into a few gotchas with some resting state data, and wanted to know if there are any problems specific to processing resting state data that can be easily avoided?
For example, here's the file structure: Project root: /home/chris/resting
Anatomical data root ($SUBJECTS_DIR): /home/chris/resting/anat
Functional data root ($FUNCTIONALS_DIR): /home/chris/resting/func
Subject 1 anatomical directory: $SUBJECTS_DIR/sub00156 (already run through recon-all)
Subject 1 functional directory: $FUNCTIONALS_DIR/sub00156 contains: subjectname ("sub00156") and a nii file in a nested subdirectory: $FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz Where f.nii.gz is some resting state data (hence no paradigm files)
For my inaugural attempt, I've run anatomical data for a participant through recon-all, and was having problems registering $FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz to the surface map in $SUBJECTS_DIR/sub00156. After some trial and error and wandering through this mailing list, I found I had to first run mktemplate-sess and then register-sess (the fs-fast tutorial lead me to believe everything was automatically handled by preproc-sess). Are these deviations a foreseeable consequence of working with resting state data? Is there some documentation of important considerations for working with resting state data?
Thanks for any help,
Chris _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi there
I am running a program to generate a patient group specific template from T1 brains. I need to know which of the Free Surfer outputs will be best for creating a patient brain template. The T1 images need to be cleaned for skull, meninges and neck. My guess is brain.finalsurfs.mgz.
thanks!
Javeria.
On Mon, Nov 5, 2012 at 9:44 PM, Douglas Greve greve@nmr.mgh.harvard.eduwrote:
Hi Chris, it should have been done with preproc-sess. What was your preproc-sess command line? At some point, I had it set up so that it would go to the bold directory by default unless you used "-fsd rest". Newer versions require you to specify the FSD specifically.
doug
On 11/5/12 9:38 PM, Chris McNorgan wrote:
Hello,
I'm getting started with freesurfer. I've played around with some of the tutorial data for fs-fast (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1) and was able to follow along and successfully carry out the preprocessing exercises (which sufficed for my purposes), which also included running register-sess on the "rest" tutorial data for sess01.
I've run into a few gotchas with some resting state data, and wanted to know if there are any problems specific to processing resting state data that can be easily avoided?
For example, here's the file structure: Project root: /home/chris/resting
Anatomical data root ($SUBJECTS_DIR): /home/chris/resting/anat
Functional data root ($FUNCTIONALS_DIR): /home/chris/resting/func
Subject 1 anatomical directory: $SUBJECTS_DIR/sub00156 (already run through recon-all)
Subject 1 functional directory: $FUNCTIONALS_DIR/sub00156 contains: subjectname ("sub00156") and a nii file in a nested subdirectory: $FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz Where f.nii.gz is some resting state data (hence no paradigm files)
For my inaugural attempt, I've run anatomical data for a participant through recon-all, and was having problems registering $FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz to the surface map in $SUBJECTS_DIR/sub00156. After some trial and error and wandering through this mailing list, I found I had to first run mktemplate-sess and then register-sess (the fs-fast tutorial lead me to believe everything was automatically handled by preproc-sess). Are these deviations a foreseeable consequence of working with resting state data? Is there some documentation of important considerations for working with resting state data?
Thanks for any help,
Chris _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
yes, that is probably best
cheers Bruce On Tue, 6 Nov 2012, Javeria Ali Hashmi wrote:
Hi there I am running a program to generate a patient group specific template from T1 brains. I need to know which of the Free Surfer outputs will be best for creating a patient brain template. The T1 images need to be cleaned for skull, meninges and neck. My guess is brain.finalsurfs.mgz.
thanks!
Javeria.
On Mon, Nov 5, 2012 at 9:44 PM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Hi Chris, it should have been done with preproc-sess. What was your preproc-sess command line? At some point, I had it set up so that it would go to the bold directory by default unless you used "-fsd rest". Newer versions require you to specify the FSD specifically. doug On 11/5/12 9:38 PM, Chris McNorgan wrote: > Hello, > > I'm getting started with freesurfer. I've played around with some of > the tutorial data for fs-fast > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1) and was > able to follow along and successfully carry out the preprocessing > exercises (which sufficed for my purposes), which also included running > register-sess on the "rest" tutorial data for sess01. > > I've run into a few gotchas with some resting state data, and wanted to > know if there are any problems specific to processing resting state data > that can be easily avoided? > > For example, here's the file structure: > Project root: > /home/chris/resting > > Anatomical data root ($SUBJECTS_DIR): > /home/chris/resting/anat > > Functional data root ($FUNCTIONALS_DIR): > /home/chris/resting/func > > Subject 1 anatomical directory: > $SUBJECTS_DIR/sub00156 > (already run through recon-all) > > Subject 1 functional directory: > $FUNCTIONALS_DIR/sub00156 > contains: > subjectname ("sub00156") > and a nii file in a nested subdirectory: > $FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz > Where f.nii.gz is some resting state data (hence no paradigm files) > > For my inaugural attempt, I've run anatomical data for a participant > through recon-all, and was having problems registering > $FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz to the surface map in > $SUBJECTS_DIR/sub00156. After some trial and error and wandering through > this mailing list, I found I had to first run mktemplate-sess and then > register-sess (the fs-fast tutorial lead me to believe everything was > automatically handled by preproc-sess). Are these deviations a > foreseeable consequence of working with resting state data? Is there > some documentation of important considerations for working with resting > state data? > > Thanks for any help, > > Chris > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.-- Javeria Ali Hashmi , PhD.
Research Fellow Athinoula A. Martinos Center for Biomedical Imaging Department of Psychiatry Massachusetts General Hospital Harvard Medical School
120 Second Ave., Suite 103 Charlestown, MA 02129, USA Email: jhashmi1@nmr.mgh.harvard.edu
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Chris McNorgan -
Douglas Greve -
Javeria Ali Hashmi