Try using mri_label2vol with the ribbon.mgz file. That has a segmenentation of everything inside the white surface.
On 08/10/2017 03:58 PM, Rockers, Elijah D. wrote: > I am attempting to create a volume from a surface. My ultimate goal is > to obtain a mask that includes everything "inside" the white matter > surfaces. wm.mgz is close, but it would nicer to just get a mask from > lh.white and rh.white. I would like these masks to be in the subject's > native space. However I try the following command and see the > resulting error: > > mri_surf2vol --o coleMRI06162006/mri/lh.white.mask.mgz --mkmask --hemi > lh --identity coleMRI06162006 --template coleMRI06162006/mri/orig/orig.mgz > > gdiagno = -1 > Using identity matrix for registration > mghRead(coleMRI06162006/mri/orig/orig.mgz, -1): could not open file > mri_surf2vol ERROR: reading coleMRI06162006/mri/orig/orig.mgz header > > I'm obviously doing something wrong here, but I'm not sure what needs > to change. I used --identity because native space, and it wouldn't let > me run the command without specifying --template, which I'm not sure I > understand, because, again, target is native space. Please illuminate me, > > Thank you, > > - Eli > > Houston Methodist. Leading Medicine. > > /U.S. News & World Report/ has recognized Houston Methodist as one of > the nation’s top 20 hospitals, placing it for the second time on the > magazine’s prestigious Honor Roll. It is also designated as a Magnet > hospital for excellence in nursing. Visit us at houstonmethodist.org > <houstonmethodist.org>. Follow us at twitter.com/MethodistHosp > <twitter.com/MethodistHosp> and facebook.com/HoustonMethodist. > > ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston > Methodist and/or its relevant affiliates and may contain restricted > and privileged material for the sole use of the intended recipient(s). > Any review, use, distribution or disclosure by others is strictly > prohibited. If you are not the intended recipient (or authorized to > receive for the recipient), please contact the sender and delete all > copies of the message. Thank you. > > > > _______________________________________________ > 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.
