It will do it's best, how well depends on the size of the resection. FS it assuming that the input is an intact (though perhaps diseased) brain. Away from the resection, it will probably do ok. Near the resection, it will probably fail, but you can probably fix it manually.
doug octavian lie wrote: > > Thank you, Doug, > > One unrelated question: can I run freesurfer on postoperative T1 > MPRAGE sequences, where the relationship of the gray to white matter > (out-in) is disrupted at the site of resection? If so, can you share > any good advice on parameters to adjust? > Thank you, > > Octavian. > > > > > On Mon, Feb 27, 2012 at 10:14 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Octavian, recon-all does not use --save_distance by default. You > can have it add --save_distance to the mris_volmask command line > using the "expert options". Run recon-all with -help to get more info. > doug > > octavian lie wrote: > > Dear all, > to follow up on my prior message below, I must say that I > called the recon-all -autorecon-all command remotely through a > automatic matlab routine in which freesurfer is one leg, with > the command nohup. For some reason, when doing this, the step > mris_volmask was run without the option --save_distance hence > no ?h.dpial.ribbon.mgz fille was created. To fix this, I > manually entered the following command in the linux terminal: > mris_volmask--label_left_white 2 --label_left_ribbon 3 > --label_right_white 41 --label_right_ribbon 42 --save_ribbon > --save_distance SUB002, which created the output files needed. > Now, do you know why running recon-all -all remotely would > exclude the option --save_distance for mris_volmask. Is there > any way to fix this in the freesurfer itself, so that I do not > have to change the matlab code? > Thank you, also see my message below. > Octavian. > On Sat, Feb 25, 2012 at 6:46 PM, octavian lie > <octavian....@gmail.com <mailto:octavian....@gmail.com> > <mailto:octavian....@gmail.com > <mailto:octavian....@gmail.com>>> wrote: > > Dear Bruce & FreeSurfers, > I ran freesurfer (86x64_64 centos version 5.1.0) on my > new linux > box (Ubuntu 11.10 64 bit, NVIDIA GEforce GTX 580, no CUDA > for now) > using recon-all -all; it went on for 8 hours, I got the message > (Recon complete without errors) in the output.txt file in my > subject directory. However, when trying to use mri_convert or > tkmedit to see the lh.dpial.ribbon.mgz, there was an error > (could > not open file). I searched for the file in all the /mri > folder and > the whole file system on my box, could not find it. I found > lh.ribbon.mgz, rh.ribbon.mgz, and ribbon.mgz, but not the > dpial.ribbon.mgz file or any other ?.ribbon.mgz variety. > I appreciate your suggestions. > Octavian. > > > > ------------------------------------------------------------------------ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 > <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > > > 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. > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
