can you try it on a linux machine? On Mon, 23 Apr 2012, Andrew C Yourich wrote:
> I have encountered this issue running Freesurfer 5.1.0 on both a Mac Pro > running Mac OS 10.6.8 as well as a Dell PC running Freesurfer using the > Ubuntu virtual machine package provided for Windows (OS was Windows XP). > > I'm going to attempt run the command exactly as you wrote it in the e-mail to > Alex and then view it in freeview to see if anything has changed. > > Thanks, > Andrew > ________________________________________ > From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] > Sent: Sunday, April 22, 2012 9:10 AM > To: Andrew C Yourich > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mris_expand not working since upgrading to v.5.1.0 > > Hi Andrew, > > I just tried this and it worked fine for me. If you tell me what > os/hardware you are running on I'll send you a current binary and you can > see if that works. > > cheers > Bruce > > p.s. do you look at the surfaces via: > > freeview -f lh.white lh.white.expanded > > On Fri, 20 Apr 2012, Andrew C > Yourich wrote: > >> >> Hello, >> >> >> >> I have recently upgraded from running version 4.0.2 of Freesurfer to the >> most current version (v.5.1.0), and have encountered a problem. I used to be >> able to expand the recon-all generated white matter volume by a percentage >> of the grey matter thickness using mris_expand, but ever since changing to >> the most current version, the mris_expand command is not returning correct >> results. The command I use is: >> >> >> >> mris_expand -thickness ./lh.white $1 lh.white.expanded >> >> >> >> where $1 is a variable indicating the percentage I wish to expand by. Since >> the version change, mris_expand does not seem to actually change the volume >> of lh.white, with the output file lh.white.expanded looking identical to >> lh.white after running the command. This occurs regardless of the value I >> enter for $1 (be it very large, very small, or even negative) The command >> appears to run normally as it did in v.4.0.2 and does not give any error >> message, but the output volume appears unchanged from the input volume. >> >> >> >> Have the parameters or flags for this command changed between the versions, >> or has mris_expand been deprecated? If so, what flags or command should I >> use instead? >> >> >> >> Thanks, >> >> >> >> - Andrew >> >> >> > > > 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. > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
