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:

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.