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

Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you.

No problem. Keeps us on our toes.

On Fri, 2008-12-12 at 14:47 -0600, Hans Johnson wrote:

Sorry for the noise.

This was a bug in our distribution system where version 4.05 was being installed in /opt/freesurfer-4.1.0. It is a bug on our end.

Thanks for helping us figure this out.

Hans

On 12/12/08 6:38 PM, "Greg Harris" gregory-harris@uiowa.edu 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

Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you.