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 < ryanhutten2...@u.northwestern.edu> wrote: > > > ---------- Forwarded message ---------- > From: Ryan Hutten <ryanhutten2...@u.northwestern.edu> > Date: Thu, Jun 30, 2011 at 1:34 PM > Subject: Re: [Freesurfer] error using recon-all function > To: Krish Subramaniam <kr...@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 < > kr...@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 < >>>> fis...@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 < >>>> fis...@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, >>>> > >>>> ______________________________**_________________ >>>> Freesurfer mailing list >>>> Freesurfer@nmr.mgh.harvard.edu >>>> >>>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>>> >>>> >>>> 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<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. >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> >> > >
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