Hi Bronwyn,
I would guess that there has been a problem with the way you run the base.
Take one case, copy the cross sectionals into a new directory and re-run
the base from scratch.
If your two time points are named like: TPID_001 and TPID_002 then the
base command should be:
recon-all -base BASEID -tp TPID_001 -tp TPID_002 -all
this will create a directory called BASEID.
Then the longitudinal commands will be:
recon-all -long TPID_001 BASEID -all
and
recon-all -long TPID_002 BASEID -all
I am a little irritated by the way you call your base (as it looks like
you called it BASEID_001. If 001 is the subject ID, then this makes
sense, but then the time point ID , TPID_001 does not. It is missing an
index for the time point like TPID_001_01 for the first and TPID_001_02
for the next etc. Please let me know how you call your input data and
base IDS. Also how many time points do you have per subject.
Best, Martin
Am 18.08.2017 um 03:01 schrieb Bruce Fischl:
Hi Bronwyn
I defer to Martin :)
Bruce
On Fri, 18 Aug 2017, Bronwyn Overs wrote:
Hi Bruce,
Please find attached both the command line output and the recon-all
log. The command line I ran was:
recon-all -long BASEID_001 TPID_001 -all
I have already run and reviewed the cross-sectional and base images
for this subject and am now at the point of running the longitudinal
image for the first time. This is one of 25 longitudinal images that
exited with the same error.
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/>
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On 18 Aug 2017, at 12:57 am, Bruce Fischl
<fis...@nmr.mgh.harvard.edu> wrote:
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 <http://neura.edu.au/>
Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe
to the
NeuRA Magazine
On 17 Aug 2017, at 2:39 pm, Bronwyn Overs <b.ov...@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 <http://neura.edu.au/>
Follow @neuraustralia on twitter Follow NeuRA on facebook Subscribe to
the NeuRA Magazine
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