Sadly, I haven't been able to determine the problem yet. I have tested the exact command that was suggested in both the Mac 5.1.0 version as well as the Windows/Ubuntu 5.1.0 virtual machine version, and neither have seemed to expand correctly when viewed in freeview. I won't have access to a machine running Linux natively until tomorrow. A colleague who runs Freesurfer 5.0 and 5.1.0 on a Linux machine is going to work with me to test if he has this issue as well.
Do you know if there have been any changes to the code of the mris_expand binary since 4.0.2? If not, we may try using the mris_expand from that version on the recon-all results from a 5.1.0 segmentation to see if the issue truly is the expand binary or not. Any other suggestions you all have would be appreciated. Thanks, Andrew ________________________________________ From: Alexandre Gramfort [gramf...@nmr.mgh.harvard.edu] Sent: Tuesday, April 24, 2012 3:24 PM To: Andrew C Yourich Subject: Fwd: Fwd: Freesurfer Digest, Vol 98, Issue 29 hi, have you fixed your problem? I still don't manage to make it work… thanks Alex ---------- Forwarded message ---------- From: Alexandre Gramfort <gramf...@nmr.mgh.harvard.edu> Date: Mon, Apr 23, 2012 at 7:10 PM Subject: Re: Fwd: Freesurfer Digest, Vol 98, Issue 29 To: Bruce Fischl <fis...@nmr.mgh.harvard.edu> Cc: Nick Schmansky <ni...@nmr.mgh.harvard.edu>, ayour...@uab.edu, Krish Subramaniam <kr...@nmr.mgh.harvard.edu>, Ruopeng Wang <rpw...@nmr.mgh.harvard.edu> > not sure about the mac, I'll cc Nick, Krish and Ruopeng so that they can > answer. could be due to my update of XCode this morning but things work fine with freeview -f lh.white -v ../mri/T1.mgz on my mac with lion. sorry for the noise > I built my own in ~fischl/dev/freesurfer/bin/freeview. Sure, put the > surfaces somewhere I can look at them and I'll take a look see the files in : /homes/6/gramfort/cluster/work/data/MNE-sample-data/subjects/fsaverage/surf/lh.white.expanded that's the sample data we use for MNE. the log: $ mris_expand -thickness lh.white 0.5 lh.white.expanded using distance as a % of thickness expanding surface lh.white by 50.0% of thickness and writing it to lh.white.expanded reading thickness... ending sse = 4485.856144 nrounds = 6 writing expanded surface to lh.white.expanded... writing group avg surface area 822 cm^2 into surface file surface expansion took 27 minutes and 15 seconds. Alex 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
