try opening it in tksurfer and see if it complains
On Sun, 2 Aug 2015, Fidel
Alfaro Almagro wrote:
Hi,
Thanks for the quick answer.
There was no error message in the previous steps.
I started it with : mris_sphere -seed 1234 ../surf/lh.inflated
../surf/lh.sphere
Although if the seed is the same, I am guessing that any non-deterministic
process would have the same output.
Is there a a way to automatically know if there was a problem in the sphere
creation?
Cheers.
2015-08-02 16:27 GMT+01:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
hmm, something seems to be wrong maybe the the ?h.sphere. Can
you try recreating it
cheers
Bruce
On Sun, 2 Aug 2015, Fidel Alfaro Almagro wrote:
Hi all,
I received an error in one of the steps of
recon-all. The error is "No such
file or directory" at the end of one of the
registration processes.
The step was mris_register -curv. The command was:
mris_register -curv ../surf/lh.sphere
<FS_DIR>/average/lh.average.curvature.filled.buckner40.tif
../surf/lh.sphere.reg
I already checked that ../surf/lh.sphere and
<FS_DIR>/average/lh.average.curvature.filled.buckner40.tif
exist (and are
readable). I also checked that the output directorry
(../surf/ ) has the
proper permisons to write.
The version of mris_register is "stable5".
Finally, the complete output message is (Please,
note that the parts with <>
have been edited by me for privacy reasons:
#--------------------------------------------
#@# Surf Reg lh Sun Aug 2 00:52:59 BST 2015
<SUBJECT_DIR>/scripts
mris_register -curv ../surf/lh.sphere
<FS_DIR>/average/lh.average.curvature.filled.buckner40.tif
../surf/lh.sphere.reg
using smoothwm curvature for final 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 ../surf/lh.sphere...
reading template parameterization from
<FS_DIR>/average/lh.average.curvature.filled.buckner40.tif...
MRISregister() -------
max_passes = 4
min_degrees = 0.500000
max_degrees = 64.000000
nangles = 8
tol=5.0e-01, sigma=0.0, host=<HOST>., nav=1024,
nbrs=1, l_extern=10000.000,
l_parea=0.200, l_nlarea=1.000, l_corr=1.000,
l_dist=5.000
using quadratic fit line minimization
complete_dist_mat 0
rms 0
smooth_averages 0
remove_neg 0
ico_order 0
which_surface 0
target_radius 0.000000
nfields 0
scale 0.000000
desired_rms_height -1.000000
momentum 0.950000
nbhd_size -10
max_nbrs 10
niterations 25
nsurfaces 0
SURFACES 3
flags 16 (10)
use curv 16
no sulc 0
no rigid align 0
mris->nsize 1
mris->hemisphere 0
randomSeed 0
tol=5.0e-01, sigma=0.0, host=<HOST>., nav=1024,
nbrs=1, l_extern=10000.000,
l_parea=0.200, l_nlarea=1.000, l_corr=1.000,
l_dist=5.000
using quadratic fit line minimization
--------------------
1 Reading lh.sulc
curvature mean = -0.000, std = 0.575
curvature mean = 0.028, std = 0.935
curvature mean = -0.002, std = 0.850
Starting MRISrigidBodyAlignGlobal()
d=64.00 min @ (16.00, 32.00, -64.00) sse =
463438.8, tmin=0.7880
d=16.00 min @ (0.00, -4.00, 4.00) sse = 460445.8,
tmin=2.3467
d=8.00 min @ (0.00, 0.00, -2.00) sse = 460199.6,
tmin=3.1967
d=4.00 min @ (0.00, 0.00, 1.00) sse = 459864.8,
tmin=4.0376
d=2.00 min @ (-0.50, -0.50, 0.00) sse = 459815.2,
tmin=4.8841
d=1.00 min @ (0.00, -0.25, 0.25) sse = 459808.6,
tmin=5.7246
d=0.50 min @ (0.12, 0.38, -0.38) sse = 459786.2,
tmin=6.5623
mrisComputeCorrelationTerm: delta is not finite at
vno 0
MRISrigidBodyAlignGlobal() done 6.56 min
No such file or directory
Linux <HOST> 2.6.32-431.el6.x86_64 #1 SMP Sun Nov 10
22:19:54 EST 2013
x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 1398979 exited with ERRORS at Sun Aug
2 01:00:20 BST 2015
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Thanks in advance.
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