Hi Anastasia, I ran: - bedpostx /media/vivi/images/freesurfer/000000112288Proc/dmri
and got the following output: subjectdir is /media/vivi/images/freesurfer/000000112288Proc/dmri Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage But before it told me that /bin/fsl_sub was mising, so i copied from where i had it to there, and then it arrived at the same place than before then I ran - fsl4.1-bedpostx /media/vivi/images/freesurfer/000000112288Proc/dmri I made symbolic link from fsl4.1-whatever to whatever. Im working in ubuntu 11.04 and I installed fsl from the package manager. and I got this: subjectdir is /media/vivi/images/freesurfer/000000112288Proc/dmri Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage 0 slices processed What should I do? Thanks! Viviana On Wed, Apr 25, 2012 at 12:52 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Viviana - I cannot replicate this on our systems but I think I know > what your system may be fussy about and I'll amend it. For now, if you > don't get any outputs can you please try running bedpostx directly on > /media/vivi/images/freesurfer/**000000112288Proc/dmri and see if that > works? > > Thanks for bringing this to our attention, > a.y > > > On Mon, 23 Apr 2012, Viviana Siless wrote: > > Hello Anastasia, >> It fixed the bug. Thank you so much! >> >> Now Im running trac-all -bedp -c >> >> But it's been running for already 3 days, and it just printed that: >> >> > trac-all -bedp -c /media/vivi/images/freesurfer/**dmrirc.example >> INFO: SUBJECTS_DIR is /media/vivi/images/freesurfer >> INFO: Diffusion root is /media/vivi/images/freesurfer >> Actual FREESURFER_HOME /media/vivi/code/freesurfer >> ln -sf /media/vivi/images/freesurfer/**000000112288Proc/dlabel/diff/** >> anat_brain_mask.flt.nii.gz >> /media/vivi/images/freesurfer/**000000112288Proc/dmri/nodif_** >> brain_mask.nii.gz >> ln -sf /media/vivi/images/freesurfer/**000000112288Proc/dmri/dwi.nii.**gz >> /media/vivi/images/freesurfer/**000000112288Proc/dmri/data.**nii.gz >> WARN: Running FSL's bedbost locally - this might take a while >> WARN: It is recommended to run this step on a cluster >> bedpostx_seychelles /media/vivi/images/freesurfer/**000000112288Proc/dmri >> subjectdir is /media/vivi/images/freesurfer/**000000112288Proc/dmri >> Making bedpostx directory structure >> Queuing preprocessing stages >> [: 223: NONE: unexpected operator >> [: 314: NONE: unexpected operator >> [: 327: xbedpostx_pre: unexpected operator >> [: 486: x: unexpected operator >> [: 486: -le: argument expected >> Queuing parallel processing stage >> >> >> Is it normal? >> Thanks for your help! (let me know if I should create another thread) >> >> Viviana Siless >> -- >> Parietal Team, INRIA Saclay >> Neurospin, Centre CEA de Saclay >> 91191 Gif sur Yvette – FRANCE >> >> >> On Wed, Apr 18, 2012 at 1:18 AM, Anastasia Yendiki < >> ayend...@nmr.mgh.harvard.edu> wrote: >> >> Hi Viviana - I suspect it may be b/c you're using the 2mm-resolution >> MNI template brain, and our atlas was built using the 1mm one. From your >> dmrirc file: >> >> # MNI template (the only option for inter-subject registration in >> this version) >> # Default: $FSLDIR/data/standard/MNI152_**T1_1mm_brain.nii.gz >> # >> #set mnitemp = /path/to/mni_template.nii.gz >> set mnitemp = /usr/share/fsl/4.1/data/** >> standard/MNI152_T1_2mm_brain.**nii.gz >> >> Can you please try changing the above from 2mm to 1mm and see if it >> works? If so, I'll make sure this is handled more elegantly in the next >> version. >> >> Hope this helps, >> a.y >> >> On Fri, 6 Apr 2012, Viviana Siless wrote: >> >> Hi Anastasia, >> Here is the data: https://transfert.inria.fr/**fichiers/** >> 4531ddb4948dff7223febc5a5b4f7e**7d/testData.tar.gz<https://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testData.tar.gz>Let >> me know if you have any >> trouble. >> I changed to the other track-all, and the error is the same. >> Please let me know if I'm doing anything wrong! >> Thank you! >> >> Viviana Siless >> -- >> Parietal Team, INRIA Saclay >> Neurospin, Centre CEA de Saclay >> 91191 Gif sur Yvette – FRANCE >> >> >> On Thu, Apr 5, 2012 at 7:38 PM, Anastasia Yendiki < >> ayend...@nmr.mgh.harvard.edu> wrote: >> >> Hi Viviana - If you upload this data set I'm happy to >> look at it. >> >> Also, I strongly recommend getting the updated version of >> trac-all from the wiki (I'm guessing from the log file that >> you're probably not using that?) See 2012/01/09 update >> here: >> >> http://surfer.nmr.mgh.**harvard.edu/fswiki/Tracula<http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula> >> >> Thanks, >> a.y >> >> >> On Wed, 4 Apr 2012, Viviana Siless wrote: >> >> Hello, >> I'm trying to run trac-all prec and I'm getting a >> segmentation fault error. >> >> Loading streamlines from /media/vivi/code/freesurfer/** >> trctrain/trc032/dlabel/mni/lh.**cst_AS.flt.trk >> Loading streamline start ROI from >> /media/vivi/code/freesurfer/**trctrain/trc033/dlabel/mni/lh.** >> cst_AS_roi1.flt.nii.gz >> Loading streamline end ROI from >> /media/vivi/code/freesurfer/**trctrain/trc033/dlabel/mni/lh.** >> cst_AS_roi2.flt.nii.gz >> Loading streamlines from /media/vivi/code/freesurfer/** >> trctrain/trc033/dlabel/mni/lh.**cst_AS.flt.trk >> INFO: Rejected 0 streamlines for straying off mask >> INFO: Rejected 0 streamlines for reversing direction >> Segmentation fault >> Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu >> SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 >> GNU/Linux >> >> trac-preproc exited with ERRORS at Wed Apr 4 18:24:21 >> CEST 2012 >> >> >> - When I look at the trak-all.error I see this error: >> >> -----------------------------**- >> SUBJECT 000000112288Proc >> DATE Wed Apr 4 18:24:21 CEST 2012 >> USER vivi >> HOST vivi-ThinkStation-C20X >> PROCESSOR x86_64 >> OS Linux >> Linux vivi-ThinkStation-C20X 2.6.38-8-generic #42-Ubuntu >> SMP Mon Apr 11 03:31:24 UTC 2011 x86_64 x86_64 x86_64 >> GNU/Linux >> $Id: trac-preproc,v 1.17.2.5 2011/05/20 06:51:51 ayendiki >> Exp $ >> /media/vivi/code/freesurfer/**bin/trac-preproc >> PWD /media/vivi/code/freesurfer >> CMD /media/vivi/code/freesurfer/**bin/dmri_train >> --outdir /media/vivi/images/freesurfer/**000000112288Proc/dlabel/mni >> --out >> lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt >> lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt >> lh.ilf_AS_avg33_mni_flt >> rh.ilf_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt >> fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt >> rh.atr_PP_avg33_mni_flt >> lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt >> lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt >> lh.slfp_PP_avg33_mni_flt >> rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt >> rh.slft_PP_avg33_mni_flt --slist >> /tmp/subj33.000000112288Proc.**16360.txt --trk >> dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk >> dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk >> dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk >> dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk >> dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk >> dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk >> dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk >> dlabel/mni/lh.slfp_PP.flt.trk >> dlabel/mni/rh.slfp_PP.flt.trk >> dlabel/mni/lh.slft_PP.flt.trk >> dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask >> dlabel/mni/cortex+2mm.nii.gz >> --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois >> dlabel/mni/lh.cst_AS_roi1.flt.**nii.gz >> dlabel/mni/lh.cst_AS_roi2.**flt.nii.gz >> dlabel/mni/rh.cst_AS_roi1.**flt.nii.gz >> dlabel/mni/rh.cst_AS_roi2.flt.**nii.gz dlabel/mni/lh.unc_AS_roi1.flt.** >> nii.gz >> dlabel/mni/lh.unc_AS_roi2.**flt.nii.gz >> dlabel/mni/rh.unc_AS_roi1.flt.**nii.gz dlabel/mni/rh.unc_AS_roi2.flt.** >> nii.gz >> dlabel/mni/lh.ilf_AS_roi1.**flt.nii.gz >> dlabel/mni/lh.ilf_AS_roi2.flt.**nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.** >> nii.gz >> dlabel/mni/rh.ilf_AS_roi2.**flt.nii.gz >> dlabel/mni/fmajor_PP_roi1.flt.**nii.gz dlabel/mni/fmajor_PP_roi2.flt.** >> nii.gz >> dlabel/mni/fminor_PP_roi1.**flt.nii.gz >> dlabel/mni/fminor_PP_roi2.flt.**nii.gz dlabel/mni/lh.atr_PP_roi1.flt.** >> nii.gz >> dlabel/mni/lh.atr_PP_roi2.**flt.nii.gz >> dlabel/mni/rh.atr_PP_roi1.flt.**nii.gz dlabel/mni/rh.atr_PP_roi2.flt.** >> nii.gz >> dlabel/mni/lh.ccg_PP_roi1.**flt.nii.gz >> dlabel/mni/lh.ccg_PP_roi2.flt.**nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.** >> nii.gz >> dlabel/mni/rh.ccg_PP_roi2.**flt.nii.gz >> dlabel/mni/lh.cab_PP_roi1.flt.**nii.gz dlabel/mni/lh.cab_PP_roi2.flt.** >> nii.gz >> dlabel/mni/rh.cab_PP_roi1.**flt.nii.gz >> dlabel/mni/rh.cab_PP_roi2.flt.**nii.gz dlabel/mni/lh.slfp_PP_roi1.** >> flt.nii.gz >> dlabel/mni/lh.slfp_PP_roi2.**flt.nii.gz >> dlabel/mni/rh.slfp_PP_roi1.**flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.** >> flt.nii.gz >> dlabel/mni/lh.slft_PP_roi1.**flt.nii.gz >> dlabel/mni/lh.slft_PP_roi2.**flt.nii.gz dlabel/mni/rh.slft_PP_roi1.** >> flt.nii.gz >> dlabel/mni/rh.slft_PP_roi2.**flt.nii.gz --bmask >> /media/vivi/images/**freesurfer/000000112288Proc/** >> dlabel/mni/aparc+aseg_mask.**nii.gz --fa >> >> /media/vivi/images/**freesurfer/000000112288Proc/**dmri/mni/dtifit_FA.flt.nii.gz >> --ncpts 5 --debug >> >> >> - If I run that command, I get the same (of course): >> >> INFO: Rejected 0 streamlines for straying off mask >> INFO: Rejected 0 streamlines for reversing direction >> Segmentation fault >> >> >> Can anybody give me an idea of the problem? I run >> recon-all and finished without errors. >> I attach the log file, the error file, and my dmrirc >> file. Please let me know if you need anything else. >> >> Thanks in advance! >> >> Viviana Siless >> -- >> Parietal Team, INRIA Saclay >> Neurospin, Centre CEA de Saclay >> 91191 Gif sur Yvette – FRANCE >> >> >> >> >> >> >> 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<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. >> >> >> >> >> >>
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