Hi again list,
Sorry I made a mistake. The lh.sphere.reg and lh.smoothwm are both in the base image directory, but I’m still receiving the mismatch error. Partial ls -l displayed below:
[b.overs@katana surf]$ ls -l $SUBJECTS_DIR/BASEID_001/surf total 120260 ... -rw-rw-r-- 1 b.overs GroupID 4554988 Aug 9 13:11 lh.qsphere.nofix -rw-rw-r-- 1 b.overs GroupID 4518556 Aug 9 13:35 lh.smoothwm -rw-rw-r-- 1 b.overs GroupID 501887 Aug 9 13:36 lh.smoothwm.BE.crv ... -rw-rw-r-- 1 b.overs GroupID 4507326 Jul 19 19:15 lh.sphere -rw-rw-r-- 1 b.overs GroupID 4507810 Jul 19 19:36 lh.sphere.reg -rw-rw-r-- 1 b.overs GroupID 501887 Aug 9 13:35 lh.sulc …
Kind regards, Bronwyn Overs Research Assistant
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
neura.edu.au http://neura.edu.au/ https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe
On 17 Aug 2017, at 2:39 pm, Bronwyn Overs b.overs@neura.edu.au wrote:
Dear freesurfer mailing list,
I have been running the recon-all -long command and received the following errors: #-------------------------------------------- #@# Surf Reg lh Wed Aug 16 18:07:26 AEST 2017 /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/TPID_001.long.BASEID_001/scripts
mris_register -curv -nosulc -norot /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.sphere.reg /usr/local/FREESURFER/freesurfer5.3.0/average/lh.average.curvature.filled.buckner40.tif ../surf/lh.sphere.reg
using smoothwm curvature for final alignment disabling initial sulc alignment... disabling initial rigid alignment... $Id: mris_register.c,v 1.59 2011/03/02 00:04:33 nicks Exp $ $Id: mrisurf.c,v 1.693.2.7 2013/05/12 22:28:01 nicks Exp $ reading surface from /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.sphere.reg... reading template parameterization from /usr/local/FREESURFER/freesurfer5.3.0/average/lh.average.curvature.filled.buckner40.tif... mrisReadTriangleFile(/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.smoothwm): surface doesn't match /mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.fix/BASEID_001/surf/lh.sphere.reg
No such file or directory mrisReadTriangleFile failed.
No such file or directory MRISreadOriginalProperties: could not read surface file smoothwm No such file or directory ERROR -5 from MRISreadOriginalProperties(). Linux katana.neura.edu.au http://katana.neura.edu.au/ 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s TPID_001.long.BASEID_001 exited with ERRORS at Wed Aug 16 18:07:29 AEST 2017
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
I checked the surf folder and the lh.sphere.reg file does not appear to be there. Do you know how this could have happened and how I can fix the problem? Kind regards, Bronwyn Overs Research Assistant
Neuroscience Research Australia Margarete Ainsworth Building Barker Street Randwick Sydney NSW 2031 Australia M 0411 308 769 T +61 2 9399 1883 F +61 2 9399 1265
neura.edu.au http://neura.edu.au/ https://twitter.com/neuraustralia https://www.facebook.com/NeuroscienceResearchAustralia http://www.neura.edu.au/help-research/subscribe