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 atlas from/cell_root/software/freesurfer/dev/sys/average/lh.curvature.buckner40.fille 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
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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Fengji Geng