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
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
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Garikoitz Lerma-Usabiaga -
Nick Schmansky