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>> 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 > 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: 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 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.
