Hi Thanks guys for the reply, I have fixed this now.
ian > -----Original Message----- > From: dgw [mailto:dgwake...@gmail.com] > Sent: 07 March 2012 19:55 > To: Nick Schmansky > Cc: Ian Charest; freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: > Undefined variable > > Hi Ian, > > This is a bug in the CBU's freesurfer wrappers written at the CBU site and not > a FreeSurfer bug. Ask them to look into fixing it. Basically, the wrapper > doesn't transfer all the variables necessary for FreeSurfer to run properly. > The only work around for you at the moment would be to run it locally i.e. > not use the CBU's wrappers. > > D > > Nick Schmansky wrote: > > are there other mni tools installed? are the variables from the > > different freesurfer installs getting mixed? > > > > n. > > > > On Wed, 2012-03-07 at 19:01 +0000, Ian Charest wrote: > >> Hi again > >> > >> > >> > >> More on this note: > >> > >> > >> > >> Using the previous stable version 4.3.0 that I have installed here, I > >> have absolutely no problem in running the same process. > >> > >> > >> > >> ian > >> > >> > >> > >> From: freesurfer-boun...@nmr.mgh.harvard.edu > >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ian > >> Charest > >> Sent: 07 March 2012 18:09 > >> To: freesurfer@nmr.mgh.harvard.edu > >> Subject: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: > >> Undefined variable > >> > >> > >> > >> > >> Hi > >> > >> > >> > >> When running recon-all I get the following error: > >> > >> > >> > >> ERROR: mpr2mni305 failed, see transforms/talairach_avi.log > >> > >> > >> > >> I called recon-all like so: > >> > >> > >> > >> recon-all > >> -i > >> > /imaging/ic01/mridata/subject01/structurals/subject01.MR.SEQUENCE.001 > >> 4.0001.2011.12.16.57.613319.8231038.IMA -all -subjid subject01 > >> > >> > >> > >> I checked the talairach_avi.log file (see the full report below), and > >> the mistake happens at the call to mpr2mni305 > >> > >> > >> > >> MPR2MNI305_TARGET: Undefined variable. > >> > >> > >> > >> I searched the mailing list for similar errors and saw a similar post > >> here: > >> > >> > >> > >> https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011- > May/01844 > >> 5.html > >> > >> > >> > >> but in this user’s case there seemed to be a problem with the MPRAGE > >> image itself (the brain seemed “squashed”) > >> > >> > >> > >> I checked the dimensions of my orig.mgz and they are ok (1x1x1). I > >> had a look at my orig.mgz in tkmedit and all seems fine. > >> > >> > >> > >> Any Idea what could be going wrong? > >> > >> > >> > >> Best Wishes > >> > >> > >> > >> Ian Charest > >> > >> > >> > >> ====== > >> > >> talairach_avi.log: > >> > >> > >> > >> /imaging/ic01/subjects/subject01/mri > >> > >> /imaging/local/software/freesurfer/5.1.0/i686//bin/talairach_avi > >> > >> --i orig.mgz --xfm transforms/talairach.auto.xfm > >> > >> $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ > >> > >> Linux l34 2.6.9-89.0.25.ELsmp #1 SMP Mon Apr 19 06:05:15 EDT 2010 > >> i686 > >> i686 i386 GNU/Linux > >> > >> Wed Mar 7 16:56:30 GMT 2012 > >> > >> /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mri_conver > >> t > >> orig.mgz talsrcimg.img > >> > >> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ > >> > >> reading from orig.mgz... > >> > >> TR=2300.00, TE=2.96, TI=900.00, flip angle=9.00 > >> > >> i_ras = (-1, 4.65661e-08, -4.09782e-08) > >> > >> j_ras = (-2.23517e-08, -3.72529e-09, -1) > >> > >> k_ras = (3.81842e-08, 1, -6.98492e-10) > >> > >> writing to talsrcimg.img... > >> > >> Analyze Output Matrix > >> > >> -1.000 -0.000 0.000 132.161; > >> > >> 0.000 -0.000 1.000 -103.886; > >> > >> -0.000 -1.000 -0.000 97.205; > >> > >> 0.000 0.000 0.000 1.000; > >> > >> -------------------- > >> > >> INFO: set hdr.hist.orient to -1 > >> > >> mpr2mni305 talsrcimg > >> > >> Wed Mar 7 16:56:34 GMT 2012 > >> > >> /imaging/local/software/freesurfer/5.1.0/i686/bin_original/mpr2mni305 > >> talsrcimg > >> > >> $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ > >> > >> MPR2MNI305_TARGET: Undefined variable. > >> > >> > >> > >> > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > 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. 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