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.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 >> 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. 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
