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