Re: [Freesurfer] FW: TRACULA re-init error
Hi - Does this directory exist? ERROR: fio_pushd: /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/mni I'd have to see the entire trac-all.log file to tell you for sure. The first error may show up earlier than the one that causes the crash. Thanks, a.y On Mon, 8 Aug 2016, Song, Daniel wrote: > > > 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/neuromi > nd/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/m > ni --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/m > ni/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 /clus > ter/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dlabel/diff --reg > /cluster/neuromind/cat/bects/subjects/pBECTS0 > 01/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/lo > wb_brain_mask.bbr.nii.gz --fa > /cluster/neuromind/cat/bects/subjects/pBECTS001/trac/pBECTS001/dmri/dtifit_FA.nii.gz > --cptd > ir /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/di > ff > 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
[Freesurfer] FW: TRACULA re-init error
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 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
