Freesurfer experts,

I emailed last week with an error using recon-all. This problem has still not been resolved. The summary of the problem should be shown below:

Thanks, Ryan

On Fri, Jul 1, 2011 at 2:06 PM, Ryan Hutten < ryanhutten2012@u.northwestern.edu> wrote:

---------- Forwarded message ---------- From: Ryan Hutten ryanhutten2012@u.northwestern.edu Date: Thu, Jun 30, 2011 at 1:34 PM Subject: Re: [Freesurfer] error using recon-all function To: Krish Subramaniam krish@nmr.mgh.harvard.edu

Krish,

under the $FREESURFER_HOME/bin directory, there is a file named avi2talxfm

I copied the output of the command you sent me.

tar -ztvf freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0.tar.gz | grep avi2tal -rwxr-xr-x root/root 2087 2011-05-22 08:28 freesurfer/bin/avi2talxfm

It looks like the file is there, but something is not working with it. Any ideas?

Thanks, Ryan

On Thu, Jun 30, 2011 at 12:53 PM, Krish Subramaniam < krish@nmr.mgh.harvard.edu> wrote:

...

Hi Ryan

We do bundle avi2talxfm in our distribution. Can you see that in $FREESURFER_HOME/bin ?

If you have the original freesurfer download file.. can you do a

tar -ztvf freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0.tar.gz | grep avi2tal

and see if it can find in the distribution ?

Krish

On 06/30/2011 01:35 PM, Bruce Fischl wrote:

...

I assume you have to install it. Nick or Krish? On Thu, 30 Jun 2011, Ryan Hutten wrote:

Is this something that I can add manually to one of the files? Please

...

let me know what steps I can take to correct this problem.

Thanks, Ryan

On Wed, Jun 29, 2011 at 1:22 PM, Bruce Fischl < fischl@nmr.mgh.harvard.edu> wrote: Nick: it looks like he's missing this command:

 tail ~/talairach_avi.log
 Reading: /usr/local/freesurfer/average/**

711-2C_as_mni_average_305.**4dfp.ifh Writing: talsrcimg_to_711-2C_as_mni_**average_305_t4_vox2vox.txt

 start time Wed Jun 29 13:05:58 CDT 2011
 end             time Wed Jun 29 13:06:19 CDT 2011

 mpr2mni305 success

 avi2talxfm orig.mgz /usr/local/freesurfer/average/**mni305.cor.mgz

talsrcimg_to_711-2C_as_mni_**average_305_t4_vox2vox.txt transforms/talairach.auto.xfm avi2talxfm: Command not found.

On Wed, 29 Jun 2011, Ryan Hutten wrote:

 I have attached the talairach_avi.log file.

 Thanks,
 Ryan

 On Wed, Jun 29, 2011 at 1:18 PM, Bruce Fischl <

fischl@nmr.mgh.harvard.edu> wrote: Hi Ryan,

      what is in transforms/talairach_avi.log?

      cheers
      Bruce



 On Wed, 29 Jun 2011, Ryan Hutten wrote:

...

Hi,

I am currently trying to use the recon-all function. It works fine on

an older computer, but my group is attempting to get freesurfer up and running on a newer computer. The subject data is

...

located in a folder called 2645166 as shown in the following command.

When I run the command:

recon-all -s 2645166 -all

I get the following error after the script runs for about a minute:

ERROR: avi2talxfm failed, see transforms/talairach_avi.log Linux dell3 2.6.35.6-45.fc14.x86_64 #1 SMP Mon Oct 18 23:57:44 UTC

2010 x86_64 x86_64 x86_64 GNU/Linux

...

The output of your bugr script gives: FREESURFER_HOME: /usr/local/freesurfer

Build stamp: freesurfer-Linux-centos4_x86_**64-stable-pub-v5.1.0

RedHat release: Fedora release 14 (Laughlin)

Kernel info: Linux 2.6.35.6-45.fc14.x86_64 x86_64

A brief internet search found nothing regarding this avi2talxfm

function. Any suggestions and/or help would be greatly appreciated.

...

Thanks,

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