Re: [Freesurfer] trakula segmentation fault
Hi Anastasia, I ran: - bedpostx /media/vivi/images/freesurfer/00112288Proc/dmri and got the following output: subjectdir is /media/vivi/images/freesurfer/00112288Proc/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/00112288Proc/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/00112288Proc/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/**00112288Proc/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/**00112288Proc/dlabel/diff/** anat_brain_mask.flt.nii.gz /media/vivi/images/freesurfer/**00112288Proc/dmri/nodif_** brain_mask.nii.gz ln -sf /media/vivi/images/freesurfer/**00112288Proc/dmri/dwi.nii.**gz /media/vivi/images/freesurfer/**00112288Proc/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/**00112288Proc/dmri subjectdir is /media/vivi/images/freesurfer/**00112288Proc/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.gzhttps://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testData.tar.gzLet 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/Traculahttp://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.
Re: [Freesurfer] trakula segmentation fault
Hi Viviana - Does it die at that point or does it keep running? If it's the latter it doesn't look wrong. For your first problem you should make sure that your path includes the bin/ directory under the FSL distribution. a.y On Wed, 25 Apr 2012, Viviana Siless wrote: Hi Anastasia, I ran: - bedpostx /media/vivi/images/freesurfer/00112288Proc/dmri and got the following output: subjectdir is /media/vivi/images/freesurfer/00112288Proc/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/00112288Proc/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/00112288Proc/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/00112288Proc/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/00112288Proc/dlabel/diff/anat_brain_mask. flt.nii.gz /media/vivi/images/freesurfer/00112288Proc/dmri/nodif_brain_mask.nii.gz ln -sf /media/vivi/images/freesurfer/00112288Proc/dmri/dwi.nii.gz /media/vivi/images/freesurfer/00112288Proc/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/00112288Proc/dmri subjectdir is /media/vivi/images/freesurfer/00112288Proc/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/4531ddb4948dff7223febc5a5b4f7e7d/testDa ta.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
Re: [Freesurfer] trakula segmentation fault
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/00112288Proc/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/00112288Proc/dlabel/diff/anat_brain_mask.flt.nii.gz /media/vivi/images/freesurfer/00112288Proc/dmri/nodif_brain_mask.nii.gz ln -sf /media/vivi/images/freesurfer/00112288Proc/dmri/dwi.nii.gz /media/vivi/images/freesurfer/00112288Proc/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/00112288Proc/dmri subjectdir is /media/vivi/images/freesurfer/00112288Proc/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/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 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 00112288Proc DATE Wed Apr 4 18:24:21 CEST 2012 USER vivi HOST
Re: [Freesurfer] trakula segmentation fault
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/00112288Proc/dlabel/diff/anat_brain_mask.flt.nii.gz /media/vivi/images/freesurfer/00112288Proc/dmri/nodif_brain_mask.nii.gz ln -sf /media/vivi/images/freesurfer/00112288Proc/dmri/dwi.nii.gz /media/vivi/images/freesurfer/00112288Proc/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/00112288Proc/dmri subjectdir is /media/vivi/images/freesurfer/00112288Proc/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.gzhttps://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testData.tar.gzLet 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/Traculahttp://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 00112288Proc 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/**00112288Proc/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
Re: [Freesurfer] trakula segmentation fault
Hi Anastasia, My mistake with the expiration date. Please try with this link: https://transfert.inria.fr/fichiers/0b1013b5de0fc0cc9e8dd2d6101a054b/testData.tar.gz Thanks! Viviana Siless -- Parietal Team, INRIA Saclay Neurospin, Centre CEA de Saclay 91191 Gif sur Yvette – FRANCE On Tue, Apr 17, 2012 at 6:03 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Viviana - I was away from email for some time and it looks like the uploaded file has expired. Could you reupload it? I apologize for the delay. Thanks, 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.gzhttps://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testData.tar.gzLet 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/Traculahttp://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 00112288Proc 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/**00112288Proc/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/subj33.00112288Proc.**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
Re: [Freesurfer] trakula segmentation fault
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/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 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 00112288Proc 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/00112288Proc/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/subj33.00112288Proc.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
Re: [Freesurfer] trakula segmentation fault
Hi Anastasia, Here is the data: https://transfert.inria.fr/fichiers/4531ddb4948dff7223febc5a5b4f7e7d/testData.tar.gzLet 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/Traculahttp://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 00112288Proc 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/**00112288Proc/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/subj33.00112288Proc.**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
Re: [Freesurfer] trakula segmentation fault
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 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 00112288Proc 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/00112288Proc/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/subj33.00112288Proc.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/00112288Proc/dlabel/mni/aparc+aseg_mask.nii.gz --fa /media/vivi/images/freesurfer/00112288Proc/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
