Re: [Freesurfer] mri_surf2surf on edited subjects
Can you send the terminal output? Also, can you check the number of vertices in the xhemi folder and make sure that the lh in the xhemi matches the rh in the main folder? On 12/13/2017 05:13 PM, Defenderfer, Matthew K wrote: > > Hi all, > > > I am trying to transfer a surface file from fsaverage_sym space to a > recently edited individual subject's hemisphere. I previously ran > recon-all on the subject and then edited the wm, brainmask, etc. to > fix some defects I had found. Before the edits, I could transfer the > surface and load it on the subject's hemisphere as an overlay > perfectly fine. After editing and rerunning the subject through > recon-all and the xhemi pipeline, I tried to transfer and load the > overlay again using the following command, same as originally: > > > mri_surf2surf --srcsubject fsaverage_sym --srcsurfreg sphere.reg > --trgsubject subj001 --trgsurfreg fsaverage_sym.sphere.reg --hemi lh > --sval template.sym.mgh --tval subj001/surf/template.sym.mgh > > > The command completes, but the resulting overlay does not have the > same number of vertices as the surface. It does however, have the same > number of vertices as the original surface from before rerunning the > recon-all command. So it seems like it's still transferring the > overlay to original surface. My SUBJECTS_DIR does not have the > subjects' original recon-all data in it either, just the data from the > edited recon-all. Any help on this would be appreciated. Thank you! > > > -Matt Defenderfer > > > *Matthew K. Defenderfer B.S. | Graduate Research Assistant* > > Graduate Biomedical Sciences|Neuroscience > > UAB | The University of Alabama at Birmingham > > Laboratory of Kristina Visscher, PhD > > Department of Neurobiology > > CIRC 111 | C: (865) 805-6389 > > > > > ___ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] mri_surf2surf on edited subjects
The number of vertices match between the lh.sphere.reg and lh.pial. All of the timestamps are the same as well. I just tried this with v5.3 as well and the problem is the same. Thank you for helping with this! -Matt Defenderfer Matthew K. Defenderfer B.S. | Graduate Research Assistant Graduate Biomedical Sciences | Neuroscience UAB | The University of Alabama at Birmingham Laboratory of Kristina Visscher, PhD Department of Neurobiology CIRC 111 | C: (865) 805-6389 From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent: Wednesday, December 13, 2017 4:16:03 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_surf2surf on edited subjects Hi Matt can you run mris_euler_number on that subject's lh.sphere.reg and see if it has the same number of vertices as the lh.pial for example? Or check timestamps. If it was not recreated after your editing you will need to rerun part of recon-all cheers Bruce On Wed, 13 Dec 2017, Defenderfer, Matthew K wrote: > > Hi all, > > > I am trying to transfer a surface file from fsaverage_sym space to a recently > edited individual > subject's hemisphere. I previously ran recon-all on the subject and then > edited the wm, brainmask, etc. > to fix some defects I had found. Before the edits, I could transfer the > surface and load it on the > subject's hemisphere as an overlay perfectly fine. After editing and > rerunning the subject through > recon-all and the xhemi pipeline, I tried to transfer and load the overlay > again using the following > command, same as originally: > > > mri_surf2surf --srcsubject fsaverage_sym --srcsurfreg sphere.reg --trgsubject > subj001 --trgsurfreg > fsaverage_sym.sphere.reg --hemi lh --sval template.sym.mgh --tval > subj001/surf/template.sym.mgh > > > The command completes, but the resulting overlay does not have the same > number of vertices as the > surface. It does however, have the same number of vertices as the original > surface from before > rerunning the recon-all command. So it seems like it's still transferring the > overlay to original > surface. My SUBJECTS_DIR does not have the subjects' original recon-all data > in it either, just the > data from the edited recon-all. Any help on this would be appreciated. Thank > you! > > > -Matt Defenderfer > > > Matthew K. Defenderfer B.S. | Graduate Research Assistant > > Graduate Biomedical Sciences | Neuroscience > > UAB | The University of Alabama at Birmingham > > Laboratory of Kristina Visscher, PhD > > Department of Neurobiology > > CIRC 111 | C: (865) 805-6389 > > > > ___ 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] mri_surf2surf on edited subjects
Hi Matt can you run mris_euler_number on that subject's lh.sphere.reg and see if it has the same number of vertices as the lh.pial for example? Or check timestamps. If it was not recreated after your editing you will need to rerun part of recon-all cheers Bruce On Wed, 13 Dec 2017, Defenderfer, Matthew K wrote: Hi all, I am trying to transfer a surface file from fsaverage_sym space to a recently edited individual subject's hemisphere. I previously ran recon-all on the subject and then edited the wm, brainmask, etc. to fix some defects I had found. Before the edits, I could transfer the surface and load it on the subject's hemisphere as an overlay perfectly fine. After editing and rerunning the subject through recon-all and the xhemi pipeline, I tried to transfer and load the overlay again using the following command, same as originally: mri_surf2surf --srcsubject fsaverage_sym --srcsurfreg sphere.reg --trgsubject subj001 --trgsurfreg fsaverage_sym.sphere.reg --hemi lh --sval template.sym.mgh --tval subj001/surf/template.sym.mgh The command completes, but the resulting overlay does not have the same number of vertices as the surface. It does however, have the same number of vertices as the original surface from before rerunning the recon-all command. So it seems like it's still transferring the overlay to original surface. My SUBJECTS_DIR does not have the subjects' original recon-all data in it either, just the data from the edited recon-all. Any help on this would be appreciated. Thank you! -Matt Defenderfer Matthew K. Defenderfer B.S. | Graduate Research Assistant Graduate Biomedical Sciences | Neuroscience UAB | The University of Alabama at Birmingham Laboratory of Kristina Visscher, PhD Department of Neurobiology CIRC 111 | C: (865) 805-6389 ___ 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.
[Freesurfer] mri_surf2surf on edited subjects
Hi all, I am trying to transfer a surface file from fsaverage_sym space to a recently edited individual subject's hemisphere. I previously ran recon-all on the subject and then edited the wm, brainmask, etc. to fix some defects I had found. Before the edits, I could transfer the surface and load it on the subject's hemisphere as an overlay perfectly fine. After editing and rerunning the subject through recon-all and the xhemi pipeline, I tried to transfer and load the overlay again using the following command, same as originally: mri_surf2surf --srcsubject fsaverage_sym --srcsurfreg sphere.reg --trgsubject subj001 --trgsurfreg fsaverage_sym.sphere.reg --hemi lh --sval template.sym.mgh --tval subj001/surf/template.sym.mgh The command completes, but the resulting overlay does not have the same number of vertices as the surface. It does however, have the same number of vertices as the original surface from before rerunning the recon-all command. So it seems like it's still transferring the overlay to original surface. My SUBJECTS_DIR does not have the subjects' original recon-all data in it either, just the data from the edited recon-all. Any help on this would be appreciated. Thank you! -Matt Defenderfer Matthew K. Defenderfer B.S. | Graduate Research Assistant Graduate Biomedical Sciences | Neuroscience UAB | The University of Alabama at Birmingham Laboratory of Kristina Visscher, PhD Department of Neurobiology CIRC 111 | C: (865) 805-6389 ___ 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.
