I have encountered this issue running Freesurfer 5.1.0 on both a Mac Pro running Mac OS 10.6.8 as well as a Dell PC running Freesurfer using the Ubuntu virtual machine package provided for Windows (OS was Windows XP).

I'm going to attempt run the command exactly as you wrote it in the e-mail to Alex and then view it in freeview to see if anything has changed.

Thanks, Andrew ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Sunday, April 22, 2012 9:10 AM To: Andrew C Yourich Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_expand not working since upgrading to v.5.1.0

Hi Andrew,

I just tried this and it worked fine for me. If you tell me what os/hardware you are running on I'll send you a current binary and you can see if that works.

cheers Bruce

p.s. do you look at the surfaces via:

freeview -f lh.white lh.white.expanded

On Fri, 20 Apr 2012, Andrew C Yourich wrote:

Hello,

I have recently upgraded from running version 4.0.2 of Freesurfer to the most current version (v.5.1.0), and have encountered a problem. I used to be able to expand the recon-all generated white matter volume by a percentage of the grey matter thickness using mris_expand, but ever since changing to the most current version, the mris_expand command is not returning correct results. The command I use is:

mris_expand -thickness ./lh.white $1 lh.white.expanded

where $1 is a variable indicating the percentage I wish to expand by. Since the version change, mris_expand does not seem to actually change the volume of lh.white, with the output file lh.white.expanded looking identical to lh.white after running the command. This occurs regardless of the value I enter for $1 (be it very large, very small, or even negative) The command appears to run normally as it did in v.4.0.2 and does not give any error message, but the output volume appears unchanged from the input volume.

Have the parameters or flags for this command changed between the versions, or has mris_expand been deprecated? If so, what flags or command should I use instead?

Thanks,

• Andrew

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I personally do not have access to a Linux machine, but I do know someone in our department that does run freesurfer on one. I had e-mailed him on Friday to see if he encountered this issue as well, so let me follow up with him and see if he is able to check mris_expand results on his computer.

- Andrew ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Monday, April 23, 2012 9:44 AM To: Andrew C Yourich Cc: freesurfer@nmr.mgh.harvard.edu; Robert C Knowlton; gramfort@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] mris_expand not working since upgrading to v.5.1.0

can you try it on a linux machine? On Mon, 23 Apr 2012, Andrew C Yourich wrote:

I have encountered this issue running Freesurfer 5.1.0 on both a Mac Pro running Mac OS 10.6.8 as well as a Dell PC running Freesurfer using the Ubuntu virtual machine package provided for Windows (OS was Windows XP).

I'm going to attempt run the command exactly as you wrote it in the e-mail to Alex and then view it in freeview to see if anything has changed.

Thanks, Andrew ________________________________________ From: Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Sunday, April 22, 2012 9:10 AM To: Andrew C Yourich Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_expand not working since upgrading to v.5.1.0

Hi Andrew,

I just tried this and it worked fine for me. If you tell me what os/hardware you are running on I'll send you a current binary and you can see if that works.

cheers Bruce

p.s. do you look at the surfaces via:

freeview -f lh.white lh.white.expanded

On Fri, 20 Apr 2012, Andrew C Yourich wrote:

...

Hello,

I have recently upgraded from running version 4.0.2 of Freesurfer to the most current version (v.5.1.0), and have encountered a problem. I used to be able to expand the recon-all generated white matter volume by a percentage of the grey matter thickness using mris_expand, but ever since changing to the most current version, the mris_expand command is not returning correct results. The command I use is:

mris_expand -thickness ./lh.white $1 lh.white.expanded

where $1 is a variable indicating the percentage I wish to expand by. Since the version change, mris_expand does not seem to actually change the volume of lh.white, with the output file lh.white.expanded looking identical to lh.white after running the command. This occurs regardless of the value I enter for $1 (be it very large, very small, or even negative) The command appears to run normally as it did in v.4.0.2 and does not give any error message, but the output volume appears unchanged from the input volume.

Have the parameters or flags for this command changed between the versions, or has mris_expand been deprecated? If so, what flags or command should I use instead?

Thanks,

• Andrew

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.