[Freesurfer] mri_vol2surf wrong hemisphere
Hi, I have a strange issue I can't figure out. I am currently trying to use the parcellation from Gordon et al. 2014 (download link here<http://www.nil.wustl.edu/labs/petersen/Resources.html>) to create ROIs for the frontoparietal network. They provided a volume of the parcellation in MNI152 space for public use. I took this volume and applied the mri_vol2surf command to it to create 2 overlays of the parcels, 1 for each hemisphere. The code was: mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage --mni152reg --o lh.Parcels_fsaverage_111.mgh --hemi lh mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage --mni152reg --o rh.Parcels_fsaverage_111.mgh --hemi rh The code ran, but the LH parcels in the volume were transferred to the RH on the surface and vice versa. This is a problem since the parcellation is not symmetric across hemispheres.This is not a problem with the volume either as I looked at it overlayed with the MNI152 brain in fslview and saw that the parcels were on the correct hemisphere. Another problem is that 1 of the frontoparietal parcels, number 24, was not found on the surface of either hemisphere after turning it to a surface. I don't know why this would be the case since there are all cortical parcels. I have also tried this with a volume ROI that is only located on the left hemisphere. After running essentially the same vol2surf command as above, the ROI only appeared on the RH surface. I am using mri_vol2surf from Freesurfer v6.0.0 Any help would be greatly appreciated. Thank you! Best, Matthew 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_vol2surf wrong hemisphere
Hi, I have a strange issue I can't figure out. I am currently trying to use the parcellation from Gordon et al. 2014 (http://www.nil.wustl.edu/labs/petersen/Resources.html) to create ROIs for the frontoparietal network. They provided a volume of the parcellation in MNI152 space for public use. I took this volume and applied the mri_vol2surf command to it to create 2 overlays of the parcels, 1 for each hemisphere. The code was: mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage --mni152reg --o lh.Parcels_fsaverage_111.mgh --hemi lh mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage --mni152reg --o rh.Parcels_fsaverage_111.mgh --hemi rh The code ran, but the LH parcels in the volume were transferred to the RH on the surface and vice versa. This is a problem since the parcellation is not symmetric across hemispheres.This is not a problem with the volume either as I looked at it overlayed with the MNI152 brain in fslview and saw that the parcels were on the correct hemisphere. Another problem is that 1 of the frontoparietal parcels, number 24, was not found on the surface of either hemisphere after turning it to a surface. I don't know why this would be the case since there are all cortical parcels. I have also tried this with a volume ROI that is only located on the left hemisphere. After running essentially the same vol2surf command as above, the ROI only appeared on the RH surface. I am using mri_vol2surf from Freesurfer v6.0.0 Any help would be greatly appreciated. Thank you! Best, Matthew 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.
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_vol2surf wrong hemisphere
Hi Doug, FSLView gives a label of L and R and the parcels on the LH in fslview match the LH parcels in their included Excel spreadsheet. That's really all the verification I have for it right now. It's possible they switched the hemispheres when they made the original parcellation volume before making the excel sheet, but I don't know how likely that is. Is there anything I can do to help out with this? -Matt 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 Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: Monday, December 4, 2017 11:46:27 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_vol2surf wrong hemisphere How do you know what is right and left in the volume? On 12/01/2017 01:59 PM, Defenderfer, Matthew K wrote: > > Hi, > > I have a strange issue I can't figure out. I am currently trying to > use the parcellation from Gordon et al. 2014 > (http://www.nil.wustl.edu/labs/petersen/Resources.html) to create ROIs > for the frontoparietal network. They provided a volume of the > parcellation in MNI152 space for public use. I took this volume and > applied the mri_vol2surf command to it to create 2 overlays of the > parcels, 1 for each hemisphere. The code was: > > mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage > --mni152reg --o lh.Parcels_fsaverage_111.mgh --hemi lh > > mri_vol2surf --mov Parcels_MNI_111.nii --trgsubject fsaverage > --mni152reg --o rh.Parcels_fsaverage_111.mgh --hemi rh > > The code ran, but the LH parcels in the volume were transferred to the > RH on the surface and vice versa. This is a problem since the > parcellation is not symmetric across hemispheres.This is not a problem > with the volume either as I looked at it overlayed with the MNI152 > brain in fslview and saw that the parcels were on the correct > hemisphere. Another problem is that 1 of the frontoparietal parcels, > number 24, was not found on the surface of either hemisphere after > turning it to a surface. I don't know why this would be the case since > there are all cortical parcels. > > I have also tried this with a volume ROI that is only located on the > left hemisphere. After running essentially the same vol2surf command > as above, the ROI only appeared on the RH surface. I am using > mri_vol2surf from Freesurfer v6.0.0 > > > Any help would be greatly appreciated. Thank you! > > Best, > Matthew 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<http://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. ___ 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] T2 white matter surface refinement
External Email - Use Caution Hi, Looking through the documentation, there are extra options to include a T2 image to refine the pial surface boundary, but I was wondering if FreeSurfer can use a T2 in conjunction with a T1 to help refine the white matter/gray matter boundary? As in, gray matter with higher myelin content than average could cause the white matter boundary to be placed further out than normal when just using a T1; can FreeSurfer currently use a T2 image to help prevent that at all? Thank you -Matt 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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
