Re: [Freesurfer] fs-fast preprocessing resting state
Hi Chris, the problem is that you do not have FSLDIR defined. Assuming you have FSL installed, then setenv FSLDIR /place/where/fsl/is/installed doug On 11/06/2012 09:09 PM, Chris McNorgan wrote: Hi Doug, Attached are two plain-text files: fslog2.txt contains the redirected terminal output after executing: preproc-sess -s sub00294 -fsd rest -per-run -surface self lhrh -mni305 -fwhm 0 ~/fslog2.txt 294files.txt contains the output of `find` for all files in the project directory related to this participant *after* executing preproc-sess, in case any clue can be found in this information (I omitted files in the log/ directory). Thanks, Chris -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
Re: [Freesurfer] fs-fast preprocessing resting state
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 gr...@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. -- 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: jhash...@nmr.mgh.harvard.edu ___ 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.
Re: [Freesurfer] fs-fast preprocessing resting state
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 gr...@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: jhash...@nmr.mgh.harvard.edu ___ 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.
Re: [Freesurfer] fs-fast preprocessing resting state
Can you send me the full terminal output? On 11/06/2012 05:39 PM, Chris McNorgan wrote: Hi Doug, Thanks for your help. To be sure of my preproc-sess line, I just ran preproc-sess on my other participant: preproc-sess -s sub00294 -fsd rest -per-run -surface self lhrh -mni305 -fwhm 0 Here's the error output from where it goes south: SNIP Tue Nov 6 16:32:30 CST 2012 mc-sess completed SUCCESSFULLY sub00294 To Surface - rawfunc2surf-sess -fwhm 0 -s sub00294 -d /home/chris/resting/func -fsd rest -self -update instem fmcpr outstem fmcpr.sm0.self.hemi -- 1/1 sub00294 1/1 sub00294 001 lh - Tue Nov 6 16:32:30 CST 2012 ERROR: cannot find /home/chris/resting/func/sub00294/rest/001/register.dof6.dat Try running register-sess with -per-run sub00294 To MNI305 - rawfunc2tal-sess -fwhm 0 -s sub00294 -d /home/chris/resting/func -fsd rest -update -subcort-mask -- 1/1 sub00294 1/1 sub00294 001 Tue Nov 6 16:32:30 CST 2012 ERROR: cannot find /home/chris/resting/func/sub00294/rest/001/register.dof6.dat Try running register-sess with -per-run Started at Tue Nov 6 16:32:25 CST 2012 Ended at Tue Nov 6 16:32:30 CST 2012 preproc-sess done /SNIP Date: Mon, 05 Nov 2012 21:44:23 -0500 From: Douglas Grevegr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fs-fast preprocessing resting state To:freesurfer@nmr.mgh.harvard.edu Message-ID:50987987.7010...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
Re: [Freesurfer] fs-fast preprocessing resting state
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.
