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: [email protected] <[email protected]> on behalf of Douglas N Greve <[email protected]> Sent: Monday, December 4, 2017 11:46:27 AM To: [email protected] 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 > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [email protected] 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 [email protected] 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.
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