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


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 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


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