Hi Bronwyn
can you send us the full command line you ran, screen output and recon-all.log? And maybe a description of where you are in the process? You already ran all the tps through the cross? And created the base?
cheers Bruce On Thu, 17 Aug 2017, Bronwyn Overs wrote:
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
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
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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.BASE ID_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.b uckner40.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.b uckner40.tif... mrisReadTriangleFile(/mridata/workingdata/CHD/BAR/PROCESSING/longitudinal.f ix/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 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
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
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
Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to the NeuRA Magazine