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
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