New subject: recon-all: core dumped error

28 Jan 2016


      Hi Bruce,
Below is our hardware/software information. Also curious, will install the newest development  version of fs 6.0 solve our problem either?
Thanks a lot!
Linux 2.6.32-573.12.1.el6.x86_64
LSB Version:       :base-4.0-amd64:base-4.0-ia32:base-4.0-noarch:core-4.0-amd64:core-4.0-ia32:core-4.0-noarch:graphics-4.0-amd64:graphics-4.0-ia32:graphics-4.0-noarch:printing-4.0-amd64:printing-4.0-ia32:printing-4.0-noarch
Distributor ID:    RedHatEnterpriseServer
Description:        Red Hat Enterprise Linux Server release 6.7 (Santiago)
Release:               6.7
Codename:        Santiago
freesurfer-Linux-centos6_x86_64-dev-20151215
----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Hi Fengji,
it's called mris_ca_label, and yes, that is what I mean. If you tell us your hardware/software environment Zeke can get you a binary
On Thu, 28 Jan 2016,
Fengji Geng wrote:
...
...
Hi Bruce,
...
...
Did you mean an updated version of mri_parcellate? If so, it would be great.
...
...
Thanks!
...
...
?
...
...

...
...
?
...
...
?
...
...
Hi Fengji
...
...
?
...
...
this is a known bug in mris_parcellate. We can give you an updated
...
version
...
...
if you want, but you should probably rerun all your subjects using it.
...
The
...
...
good news is that it's fast - just a couple of min/hemi
...
...
?
...
...
cheers
...
...
Bruce
...
...
? On Tue, 26 Jan
...
...
2016, Fengji Geng wrote:
...
...
?
...
...
...
Hello fs experts,
...
...
...
...
...
...
We ran a command like ?recon-all -all -s HMN002
...
-hippocampal-subfields-T1T2
...
...
...
HMN002/T2/*.mgz T1T2?. Then, there was an error as ?Abort (core dumped)?
...
...
...
(which is also attached below). The error log file is also attached here.?
...
...
...
...
...
...
Error msg:
...
...
...

...
...

...
...
...

...
...
...
setting seed for random number generator to 1234
...
...
...
using ../mri/aseg.presurf.mgz aseg volume to correct midline
...
...
...
$Id: mris_ca_label.c,v 1.37 2014/02/04 17:46:42 fischl Exp $
...
...
...
? $Id: mrisurf.c,v 1.775 2015/12/10 21:16:09 fischl Exp $
...
...
...
reading
...
...
atlasfrom/cell_root/software/freesurfer/dev/sys/average/lh.curvature
...
...
.buckner40.f
...
ille
...
...
...
d.desikan_killiany.2010-03-25.gcs...
...
...
...
reading color table from GCSA file....
...
...
...
average std = 1.0?? using min determinant for regularization = 0.011
...
...
...
0 singular and 384 ill-conditioned covariance matrices regularized
...
...
...
input 0: MEAN CURVATURE, flags 0, avgs 5, name mean_curvature
...
...
...
labeling surface...
...
...
...
1592 labels changed using aseg
...
...
...
relabeling using gibbs priors...
...
...
...
000:?? 2975 changed, 134786 examined...
...
...
...
001:??? 698 changed, 12707 examined...
...
...
...
002:??? 152 changed, 3873 examined...
...
...
...
003:???? 50 changed, 880 examined...
...
...
...
004:???? 29 changed, 284 examined...
...
...
...
005:???? 16 changed, 164 examined...
...
...
...
006:????? 7 changed, 87 examined...
...
...
...
007:????? 1 changed, 42 examined...
...
...
...
008:????? 0 changed, 4 examined...
...
...
...
206 labels changed using aseg
...
...
...
000: 105 total segments, 64 labels (264 vertices) changed
...
...
...
001: 43 total segments, 4 labels (14 vertices) changed
...
...
...
002: 39 total segments, 0 labels (0 vertices) changed
...
...
...
1 filter iterations complete (10 requested, 0 changed)
...
...
...
Abort (core dumped)
...
...
...
Linux hippocampus.umd.edu 2.6.32-573.12.1.el6.x86_64 #1 SMP Mon Nov
...
...
23
...
...
...
12:55:32 EST 2015 x86_64 x86_64 x86_64 GNU/Linux
...
...
...
...
...
...
recon-all -s HMN002 exited with ERRORS at Tue Jan 26 00:23:40 EST
...
...
2016
...
...
...
...
...
...
Our freesurfer information:
...
...
...
-------- freesurfer-Linux-centos6_x86_64-dev-20151215 --------
...
...
...
Setting up environment for FreeSurfer/FS-FAST (and FSL)
...
...
...
FREESURFER_HOME?? /cell_root/software/freesurfer/dev/sys
...
...
...
FSFAST_HOME?????? /cell_root/software/freesurfer/dev/sys/fsfast
...
...
...
FSF_OUTPUT_FORMAT nii.gz
...
...
...
SUBJECTS_DIR????? /export/data/hippocampus/HMN/data
...
...
...
MNI_DIR?????????? /cell_root/software/freesurfer/dev/sys/mni
...
...
...
FSL_DIR?????????? /cell_root/software/fsl/new/sys
...
...
...
...
...
...
Looking forward to hearing how we can resolve this error. Also,
...
...
thanks in
...
...
...
advance.
...
...
...
...
...
...
Best,
...
...
...
...
...
...
----- Fengji
...
...
...
...
...
...
...
...
...
?
...
...
?
...
...
?
...
...

...
...
Fengji
...
...
?
...
...
...
---
Fengji

Re: [Freesurfer] recon-all: core dumped error