thanks Alex. If anyone needs a fix before the next release let us know what hardware/software version you are running and we'll send you a binary
cheers Bruce On Wed, 25 Apr 2012, Alexandre Gramfort wrote: > hi all, > > @bruce : I've just given a try your own binaries in > > ~fischl/dev/freesurfer/bin/ > > and it worked fine. It looks like a bug has been fixed since the last > stable release. > > Alex > > On Tue, Apr 24, 2012 at 10:44 PM, Andrew C Yourich <ayour...@uab.edu> wrote: >> 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
