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: [email protected] > [mailto:[email protected]] On Behalf Of Ian > Charest > Sent: 07 March 2012 18:09 > To: [email protected] > 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.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.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. > > > > > _______________________________________________ > Freesurfer mailing list > [email protected] > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list [email protected] 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 . 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.
