Dan ________________________________ From: Ostrowski, Lauren Sent: Monday, August 08, 2016 4:08 PM To: Song, Daniel Subject: FW: TRACULA re-init error
________________________________ From: Ostrowski, Lauren Sent: Monday, August 08, 2016 4:04 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: TRACULA re-init error
Hi all,
I'm running into a problem with TRACULA, when I try to re-initialize tracts that failed to reconstruct during the first run. I have set reinit = 1 in the configuration file and specified the particular tracts that I want to reconstruct, but when I try to run the "trac-all -prior" step, I keep getting this error message:
INFO: SUBJECTS_DIR is /autofs/cluster/neuromind/cat/bects/subjects INFO: Diffusion root is /cluster/neuromind/cat/bects/subjects/pBECTS001/trac Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos6_x86_64/dev trac-preproc -c /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/scripts/dmrirc.local -log /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/scripts/trac-all.log -cmd /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/scripts/trac-all.cmd #------------------------------------- /usr/local/freesurfer/dev/bin/trac-preproc #------------------------------------- #@# Priors Mon Aug 8 15:53:46 EDT 2016 /usr/local/freesurfer/dev/bin/dmri_train --outdir /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni --out fmajor_PP_avg33_mni_bbr --slist /tmp/subj33.pBECTS001.15581.txt --trk dlabel/mni/fmajor_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 0 --rois dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz --bmask /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/dtifit_FA.nii.gz --cptdir /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/diff --reg /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/xfms/mni2diff.bbr.mat --ncpts 7 --xstr --trunc ERROR: fio_pushd: /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni
cwd /autofs/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/dlabel/mni cmdline /usr/local/freesurfer/dev/bin/dmri_train --outdir /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni --out fmajor_PP_avg33_mni_bbr --slist /tmp/subj33.pBECTS001.15581.txt --trk dlabel/mni/fmajor_PP.bbr.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 0 --rois dlabel/mni/fmajor_PP_roi1.bbr.nii.gz dlabel/mni/fmajor_PP_roi2.bbr.nii.gz --bmask /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni/lowb_brain_mask.bbr.nii.gz --fa /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/dtifit_FA.nii.gz --cptdir /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/diff --reg /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/xfms/mni2diff.bbr.mat --ncpts 7 --xstr --trunc sysname Linux hostname truffles machine x86_64 user lo941 Output directory: /autofs/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni Output directory in test subject's space: /autofs/cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/diff Output base: fmajor_PP_avg33_mni_bbr Training subject directory list: /tmp/subj33.pBECTS001.15581.txt Location of streamline files relative to base: dlabel/mni/fmajor_PP.bbr.trk Location of start ROI files relative to base: dlabel/mni/fmajor_PP_roi1.bbr.nii.gz Location of end ROI files relative to base: dlabel/mni/fmajor_PP_roi2.bbr.nii.gz Location of cortex masks relative to base: dlabel/mni/cortex+2mm.nii.gz Label ID's from aparc+aseg to add to cortex mask: 0 Location of aparc+aseg's relative to base: dlabel/mni/aparc+aseg.nii.gz Brain mask for output subject: Segmentation fault (core dumped) Linux truffles 2.6.32-573.22.1.el6.x86_64 #1 SMP Wed Mar 23 03:35:39 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Mon Aug 8 15:53:46 EDT 2016
Any help would be very much appreciated. It seems to me that TRACULA can't find the aparc+aseg labels, but when I looked at the aparc+aseg nifty file, the parcellations and labels all seem correct.
Thanks, Lauren Ostrowski