I don't know about mri_morphology, but you can use mri_binarize to erode. It has several options to allow control of how the erosion is done
On 05/22/2017 12:48 PM, Gamaliz wrote: > Douglas, > > I just realized that I was using the wrong feeesurfer output. I had 3 > processed MRIs for the same subject, and I just happened to pick the > wrong one. The output of mri_surf2vol is indeed perfectly registered > to the T1.mgz. So my problem is resolved. It still bugs me that the > --identity works even if you type anything as the subjectid, luckily > this does not affect me at all. > > > Thanks for your help. > > On another accord, I used the mri_morphology to erode the white matter > and noticed that it erodes quite a lot in a single iteration, is there > any other command which provides better controls in how much gets > eroded? Also. is the erosion always happening inwards? > > Gabriel > > On Thu, May 18, 2017 at 12:29 PM, Gamaliz <gliza...@fiu.edu > <mailto:gliza...@fiu.edu>> wrote: > > I thing I noticed is that if I change the "--identity" parameter > it provides the same result. I am just typing anything and it > still produces the same volume that gets created when the > subject_id is used. > > On Thu, May 18, 2017 at 12:16 PM, Gamaliz <gliza...@fiu.edu > <mailto:gliza...@fiu.edu>> wrote: > > Douglas, > > I am looking at them in freeview and mango. They are not > aligned. I am able to align them using flirt, and they come > out perfect. I have tried 5 cases. 3 of them they are aligned, > two were not. I am loading below the wm and lh.wm. They are > supposed to be aligned (wm is aligned with T1). > > I got a surface by using Bruce's method, but it's much more > irregular than the one obtained from mri_surf2vol. I wonder > why the inconsistency. I guess I can create the surface and > flirt using a solid transform to the T1. It takes longer, but > it works. > > Gabriel > > Inline image 1 > > > > > -- > gAbE > > > > > -- > gAbE > > > _______________________________________________ > 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.
