Nick,
Here is that data:
recon-all --version $Id: recon-all,v 1.133.2.30 2008/04/17 20:38:23 nicks Exp $
cd /opt/freesurfer harris% cat build-stamp.txt freesurfer-Darwin-leopard-i686-stable-pub-v4.0.5 harris% ls -l /opt/freesurfer lrwxr-xr-x 1 root admin 35 Nov 28 09:31 /opt/freesurfer@ -> /opt/freesurfer_v4.1.0-full_Darwin9
From this I can see that our internal propagation of directories
/opt/freesurfer_v4.1.0-full_Darwin9 was somehow based on the wrong .dmg file. We will try again at our end.
Thanks. Greg
On 12/12/08 2:02 PM, "Nick Schmansky" nicks@nmr.mgh.harvard.edu wrote:
Greg,
Does the build-stamp.txt file in your $FREESURFER_HOME say:
freesurfer-Darwin-leopard-i686-stable-pub-v4.1.0 ?
I'm puzzled as to why mri_segstats is missing from your distribution and recon-all does not recognize -segstats, as I have just now confirmed that the publicly released distribution: freesurfer-Darwin-leopard-i686-stable-pub-v4.1.0-full.dmg both contains mri_segstats, and recognizes the segstats flag. Also I have double-checked this with others who have installed this version.
Can you email me the recon-all you are using? Or just send me the output of 'recon-all --version'.
I corrected the ReleaseNotes to say -wmparc instead of -wmstats, thanks.
Nick
On Fri, 2008-12-12 at 18:38 -0600, Greg Harris wrote:
Nick,
We have yet another request regarding the MacOSX Leopard Intel version 4.1.0 download package that delivers FreeSurfer.
The program mri_segstats is not found, although it is there in the Linux package. Also, recon-all -segstats gives the 'switch not recognized' error message in MacOSX Leopard Intel, but accepts it in the recon-all in the Linux package.
I also noted that the fswiki/ReleaseNotes tells us to run recon-all -segstats -wmstats, but there is no -wmstats; what you need is -wmparc.
Until you can post the updated files, probably mri_segstats and recon-all, we will have to avoid FreeSurfing on our Macs which number about half of our compute cluster.
Thanks for your help!
Greg Harris Iowa Psychiatric NeuroImaging Consortium
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