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.0014.0001.2011.12.16.57.613319.8231038.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/018445.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-May/018445.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_convert 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.