the best option is to download the beta of v5.2 which linked from here: https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes (look for 'Get a BETA here'). i've confirmed that that atlas is contained in that release.
Nick > Hi FS experts, > I read that the current dev version for recon-all is going to be the same > to the 5.2 version, so I started a new project with the dev version (in > CentOS 4). > > I have this very strange error that I am unable to interpret, when running > mpr2mni305 in one case the target is specified as > 711-2C_as_mni_average_305, but in the dev version the target is > 3T18yoSchwartzReactN32_as_orig, this file does not exist... > > > What should I try now? > > (just in case, this is the command I launch: recon-all --i xxxxx -s > xxxxxxx > -qcache -hippo-subfields -all > > > (This is the talairach_avi.log) > ERROR WITH DEV VERSION > -------------------------------------------- > /home/glerma/FS/52/freesurfer/subjects/TNT/S_08/mri > /home/glerma/FS/52/freesurfer/bin/talairach_avi > --i orig_nu.mgz --xfm transforms/talairach.auto.xfm > $Id: talairach_avi,v 1.10 2012/07/16 15:54:03 nicks Exp $ > Linux cajal 2.6.18-164.15.1.el5 #1 SMP Wed Mar 17 11:30:06 EDT 2010 x86_64 > x86_64 x86_64 GNU/Linux > Thu Jan 24 00:26:09 CET 2013 > mri_convert orig_nu.mgz talsrcimg.img > $Id: mri_convert.c,v 1.202 2012/10/17 19:23:56 greve Exp $ > reading from orig_nu.mgz... > TR=2300.00, TE=2.97, TI=1100.00, flip angle=9.00 > i_ras = (-1, -3.03407e-09, 2.32831e-10) > j_ras = (1.16415e-10, 0, -1) > k_ras = (3.03407e-09, 1, 3.72529e-09) > writing to talsrcimg.img... > Analyze Output Matrix > -1.000 0.000 0.000 132.933; > -0.000 0.000 1.000 -105.037; > 0.000 -1.000 0.000 161.057; > 0.000 0.000 0.000 1.000; > -------------------- > INFO: set hdr.hist.orient to -1 > mpr2mni305 talsrcimg > Thu Jan 24 00:26:10 CET 2013 > /home/glerma/FS/52/freesurfer/bin/mpr2mni305 talsrcimg > $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ > target=3T18yoSchwartzReactN32_as_orig > ERROR: > /home/glerma/FS/52/freesurfer/average/3T18yoSchwartzReactN32_as_orig.4dfp.img > does not exist! > > > > > SAME SUBJECT, SAME HARD and OS, 5.0 VERSION > --------------------------------------------------------------------------------- > /home/BCBL/glerma/freesurfer/subjects/TNT/S_08/mri > /usr/local/freesurfer/bin/talairach_avi > --i nu.mgz --xfm transforms/talairach.auto.xfm > $Id: talairach_avi,v 1.7 2010/02/07 22:50:52 nicks Exp $ > Linux cajal 2.6.18-164.15.1.el5 #1 SMP Wed Mar 17 11:30:06 EDT 2010 x86_64 > x86_64 x86_64 GNU/Linux > Sat Aug 25 06:44:15 CEST 2012 > mri_convert nu.mgz talsrcimg.img > $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ > reading from nu.mgz... > TR=2300.00, TE=2.97, TI=1100.00, flip angle=9.00 > i_ras = (-1, 0, 5.55112e-17) > j_ras = (5.55112e-17, 3.72529e-09, -1) > k_ras = (4.44089e-16, 1, -1.05964e-18) > writing to talsrcimg.img... > Analyze Output Matrix > -1.000 0.000 0.000 132.933; > 0.000 0.000 1.000 -105.037; > 0.000 -1.000 -0.000 161.057; > 0.000 0.000 0.000 1.000; > -------------------- > INFO: set hdr.hist.orient to -1 > mpr2mni305 talsrcimg > Sat Aug 25 06:44:16 CEST 2012 > /usr/local/freesurfer/bin/mpr2mni305 talsrcimg > $Id: mpr2mni305,v 1.4 2009/06/03 16:01:38 nicks Exp $ > target=711-2C_as_mni_average_305 > > -------------------------------- continues....---------------------- > > > > > > and this is the setup output: > -------- freesurfer-Linux-centos4_x86_64-dev-20121127 -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /home/glerma/FS/52/freesurfer > FSFAST_HOME /home/glerma/glerma/software/freesurfer/fsfast >> older > version location > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /home/glerma/FS/52/freesurfer/subjects/TNT > MNI_DIR /home/glerma/FS/52/freesurfer/mni > FSL_DIR /usr/local/fsl > > > > many thanks! > Gari > _______________________________________________ > 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.
