glad it works, although it's a bit of a mystery why it was broken. cheers Bruce On Thu, 26 Apr 2012, Andrew C Yourich wrote:
> I've replaced my old mris_expand file with the one downloaded from the link > below, and now it is working perfectly. Thank you so much to all of you who > helped me resolve this issue. I really appreciate it. > > - Andrew > ________________________________________ > From: Nick Schmansky [ni...@nmr.mgh.harvard.edu] > Sent: Thursday, April 26, 2012 10:18 AM > To: Andrew C Yourich > Cc: Bruce Fischl; gramf...@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Fwd: Freesurfer Digest, Vol 98, Issue 29 > > i've posted a build for the mac here: > > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-leopard-intel/ > > n. > > > On Wed, 2012-04-25 at 15:02 +0000, Andrew C Yourich wrote: >> If you all have a fixed binary for a Mac Pro running Mac OS 10.6.8 that you >> would be able to forward me, I would greatly appreciate it. >> >> Thanks, >> Andrew >> ________________________________________ >> From: Bruce Fischl [fis...@nmr.mgh.harvard.edu] >> Sent: Wednesday, April 25, 2012 8:56 AM >> To: Alexandre Gramfort >> Cc: Andrew C Yourich; Robert C Knowlton; freesurfer@nmr.mgh.harvard.edu >> Subject: Re: Fwd: Freesurfer Digest, Vol 98, Issue 29 >> >> 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 >> >> > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
