---------- 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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