Re: [Freesurfer] Trakula
Hi Anastasia, Thank you very much for your help and recommendations. I will try to fix These Problems. I would like to ask you one more question. Is there any command which could help me to invert the gradient vectors for my DWI scan in the z direction? Best Bahram 2015-08-24 17:57 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - I looked at your subject's files. First, the freesurfer recon failed in the right hemisphere, probably because of a visible artifact on your T1 (see aseg screenshot). This affects the aparc+aseg, so you can't run tracula before you fix it. Second, the gradient vectors for your DWI scan probably need to be inverted in the z direction (see other screenshot with the principal eigenvectors of the tensors shown over the FA map). The vectors are oriented correctly in the axial view, but not in the sagittal or coronal view (see for example their orientation in the cingulum bundle in saggital view, where the cross-hair is centered, or in the corticospinal tract in coronal view). This is not causing your error, but you have to fix it for the tractography to work properly. Third, your DWI data has very anisotropic resolution (1.8 x 1.8 x 6.5 mm). Your voxels are almost 4 times as big in z than in x/y. This is not causing your error, but it is not optimal for diffusion analysis. Anisotropic voxels can bias estimates of diffusion anisotropy. Also, you only have 12 directions with b=1000 and the other directions were acquired with a much lower b-value (b=200). It's unlikely that you'll get reliable fits of crossing-fiber models like the one used by tracula on this data. Again, this is not causing the error you're seeing but it will make it difficult to get usable results from this DWI data. Best, a.y On Thu, 20 Aug 2015, B M wrote: Hi Anastasia, please find the files in attachment. Best regards Bahram 2015-08-19 21:55 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - There are some errors in there related to registration files. Can you please send these files? bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat Thanks, a.y On Tue, 18 Aug 2015, B M wrote: Hi Anastasia, Please find attached the trac-all.log file. Thank you very much for your help. Bahram 2015-08-17 19:31 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - Can you please send us your entire trac-all.log file? Thanks! a.y On Fri, 14 Aug 2015, B M wrote: Dear experts, I have the last version of tTrakula. i did the first step with trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc This worked properly to the end as shown below: trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015 However looking at logfile i found following errors: flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) OR Loading brain mask of output subject from /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz niiRead(): error opening file /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz ERROR: Could not read /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz AND as i tried the next step i got the following error: bm@bm-linux:~$ trac-all -bedp -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc INFO: SUBJECTS_DIR is bmdaten/Auswertung/ALS-Review/Trakula/ INFO: Diffusion root is bmdaten/Auswertung/ALS-Review/Trakula/ Actual FREESURFER_HOME /usr/local/freesurfer WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri
Re: [Freesurfer] Trakula
Hi Bahram - The gradient table is a text file with 3 columns. You need to multiply the 3rd column by -1. You can do this in matlab, awk, perl, or any scripting language that handles text files. Best, a.y On Wed, 26 Aug 2015, B M wrote: Hi Anastasia, Thank you very much for your help and recommendations. I will try to fix These Problems. I would like to ask you one more question. Is there any command which could help me to invert the gradient vectors for my DWI scan in the z direction? Best Bahram 2015-08-24 17:57 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - I looked at your subject's files. First, the freesurfer recon failed in the right hemisphere, probably because of a visible artifact on your T1 (see aseg screenshot). This affects the aparc+aseg, so you can't run tracula before you fix it. Second, the gradient vectors for your DWI scan probably need to be inverted in the z direction (see other screenshot with the principal eigenvectors of the tensors shown over the FA map). The vectors are oriented correctly in the axial view, but not in the sagittal or coronal view (see for example their orientation in the cingulum bundle in saggital view, where the cross-hair is centered, or in the corticospinal tract in coronal view). This is not causing your error, but you have to fix it for the tractography to work properly. Third, your DWI data has very anisotropic resolution (1.8 x 1.8 x 6.5 mm). Your voxels are almost 4 times as big in z than in x/y. This is not causing your error, but it is not optimal for diffusion analysis. Anisotropic voxels can bias estimates of diffusion anisotropy. Also, you only have 12 directions with b=1000 and the other directions were acquired with a much lower b-value (b=200). It's unlikely that you'll get reliable fits of crossing-fiber models like the one used by tracula on this data. Again, this is not causing the error you're seeing but it will make it difficult to get usable results from this DWI data. Best, a.y On Thu, 20 Aug 2015, B M wrote: Hi Anastasia, please find the files in attachment. Best regards Bahram 2015-08-19 21:55 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - There are some errors in there related to registration files. Can you please send these files? bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat Thanks, a.y On Tue, 18 Aug 2015, B M wrote: Hi Anastasia, Please find attached the trac-all.log file. Thank you very much for your help. Bahram 2015-08-17 19:31 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - Can you please send us your entire trac-all.log file? Thanks! a.y On Fri, 14 Aug 2015, B M wrote: Dear experts, I have the last version of tTrakula. i did the first step with trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc This worked properly to the end as shown below: trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015 However looking at logfile i found following errors: flirt -inbmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.ni i.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bb r.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) OR Loading brain mask of output subject from
Re: [Freesurfer] Trakula
Hi Anastasia, please find the files in attachment. Best regards Bahram 2015-08-19 21:55 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - There are some errors in there related to registration files. Can you please send these files? bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat Thanks, a.y On Tue, 18 Aug 2015, B M wrote: Hi Anastasia, Please find attached the trac-all.log file. Thank you very much for your help. Bahram 2015-08-17 19:31 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - Can you please send us your entire trac-all.log file? Thanks! a.y On Fri, 14 Aug 2015, B M wrote: Dear experts, I have the last version of tTrakula. i did the first step with trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc This worked properly to the end as shown below: trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015 However looking at logfile i found following errors: flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) OR Loading brain mask of output subject from /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz niiRead(): error opening file /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz ERROR: Could not read /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz AND as i tried the next step i got the following error: bm@bm-linux:~$ trac-all -bedp -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc INFO: SUBJECTS_DIR is bmdaten/Auswertung/ALS-Review/Trakula/ INFO: Diffusion root is bmdaten/Auswertung/ALS-Review/Trakula/ Actual FREESURFER_HOME /usr/local/freesurfer WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected Could you please advise me what to do? Best Bahram ___ 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. ___ 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. anat2diff.bbr.mat Description: application/extension-mat anat2mni.mat Description: application/extension-mat ___ 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.
Re: [Freesurfer] Trakula
Hi Bahram - The anatomical-to-diffusion registration matrix is all zeros, so something went wrong there. I'll need to see all the output files to investigate. Can you please zip up this subject's tracula output directories (dmri, dmri.bedpostX, dpath, dlabel, scripts) and upload everything for me here? https://gate.nmr.mgh.harvard.edu/filedrop2/ Thanks, a.y On Thu, 20 Aug 2015, B M wrote: Hi Anastasia, please find the files in attachment. Best regards Bahram 2015-08-19 21:55 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - There are some errors in there related to registration files. Can you please send these files? bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat Thanks, a.y On Tue, 18 Aug 2015, B M wrote: Hi Anastasia, Please find attached the trac-all.log file. Thank you very much for your help. Bahram 2015-08-17 19:31 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - Can you please send us your entire trac-all.log file? Thanks! a.y On Fri, 14 Aug 2015, B M wrote: Dear experts, I have the last version of tTrakula. i did the first step with trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc This worked properly to the end as shown below: trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015 However looking at logfile i found following errors: flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) OR Loading brain mask of output subject from /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz niiRead(): error opening file /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz ERROR: Could not read /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz AND as i tried the next step i got the following error: bm@bm-linux:~$ trac-all -bedp -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc INFO: SUBJECTS_DIR is bmdaten/Auswertung/ALS-Review/Trakula/ INFO: Diffusion root is bmdaten/Auswertung/ALS-Review/Trakula/ Actual FREESURFER_HOME /usr/local/freesurfer WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected Could you please advise me what to do? Best Bahram ___ 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. ___ 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
Re: [Freesurfer] Trakula
Hi Bahram - There are some errors in there related to registration files. Can you please send these files? bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2mni.mat Thanks, a.y On Tue, 18 Aug 2015, B M wrote: Hi Anastasia, Please find attached the trac-all.log file. Thank you very much for your help. Bahram 2015-08-17 19:31 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - Can you please send us your entire trac-all.log file? Thanks! a.y On Fri, 14 Aug 2015, B M wrote: Dear experts, I have the last version of tTrakula. i did the first step with trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc This worked properly to the end as shown below: trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015 However looking at logfile i found following errors: flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) OR Loading brain mask of output subject from /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz niiRead(): error opening file /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz ERROR: Could not read /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz AND as i tried the next step i got the following error: bm@bm-linux:~$ trac-all -bedp -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc INFO: SUBJECTS_DIR is bmdaten/Auswertung/ALS-Review/Trakula/ INFO: Diffusion root is bmdaten/Auswertung/ALS-Review/Trakula/ Actual FREESURFER_HOME /usr/local/freesurfer WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected Could you please advise me what to do? Best Bahram ___ 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. ___ 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.
Re: [Freesurfer] Trakula
Hi Anastasia, Please find attached the trac-all.log file. Thank you very much for your help. Bahram 2015-08-17 19:31 GMT+02:00 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Bahram - Can you please send us your entire trac-all.log file? Thanks! a.y On Fri, 14 Aug 2015, B M wrote: Dear experts, I have the last version of tTrakula. i did the first step with trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc This worked properly to the end as shown below: trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015 However looking at logfile i found following errors: flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) OR Loading brain mask of output subject from /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz niiRead(): error opening file /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz ERROR: Could not read /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz AND as i tried the next step i got the following error: bm@bm-linux:~$ trac-all -bedp -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc INFO: SUBJECTS_DIR is bmdaten/Auswertung/ALS-Review/Trakula/ INFO: Diffusion root is bmdaten/Auswertung/ALS-Review/Trakula/ Actual FREESURFER_HOME /usr/local/freesurfer WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected Could you please advise me what to do? Best Bahram ___ 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. Fri Aug 14 17:22:48 CEST 2015 /home/bm /usr/local/freesurfer/bin/trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc Subject P01-a SUBJECTS_DIR bmdaten/Auswertung/ALS-Review/Trakula/ FREESURFER_HOME /usr/local/freesurfer Actual FREESURFER_HOME /usr/local/freesurfer build-stamp.txt: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0 bm bm-linux Linux bm-linux 3.11.0-26-generic #45~precise1-Ubuntu SMP Tue Jul 15 04:02:35 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc 256954 maxlocks unlimited maxsignal256954 maxmessage 819200 maxnice 0 maxrtprio0 maxrttimeunlimited total used free sharedbuffers cached Mem: 32909372 309815561927816 0 776952 25756624 -/+ buffers/cache:4447980 28461392 Swap:124999676 9000 124990676 Program versions: $Id: trac-all,v 1.56 2014/05/26 08:28:32 ayendiki Exp $ mri_convert --all-info ProgramName: mri_convert ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/08/14-15:22:48-GMT BuildTimeStamp: Aug 16 2014 05:13:24 CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $ User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400 FLIRT version 6.0 $Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $ $Id: mri_cvs_register,v 1.15.2.12 2013/02/09 00:37:37 nicks Exp $ ProgramName: dmri_motion ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/08/14-15:22:48-GMT BuildTimeStamp: Feb 2 2013 22:46:06 CVS: User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400 ProgramName: dmri_train ProgramArguments: --all-info ProgramVersion: $Name: $ TimeStamp: 2015/08/14-15:22:48-GMT BuildTimeStamp: May 23 2014 05:15:35 CVS: User: bm Machine: bm-linux Platform: Linux PlatformVersion: 3.11.0-26-generic CompilerName: GCC CompilerVersion: 30400
Re: [Freesurfer] Trakula
Hi Bahram - Can you please send us your entire trac-all.log file? Thanks! a.y On Fri, 14 Aug 2015, B M wrote: Dear experts, I have the last version of tTrakula. i did the first step with trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc This worked properly to the end as shown below: trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015 However looking at logfile i found following errors: flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) OR Loading brain mask of output subject from /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz niiRead(): error opening file /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz ERROR: Could not read /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz AND as i tried the next step i got the following error: bm@bm-linux:~$ trac-all -bedp -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc INFO: SUBJECTS_DIR is bmdaten/Auswertung/ALS-Review/Trakula/ INFO: Diffusion root is bmdaten/Auswertung/ALS-Review/Trakula/ Actual FREESURFER_HOME /usr/local/freesurfer WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected Could you please advise me what to do? Best Bahram ___ 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.
[Freesurfer] Trakula
Dear experts, I have the last version of tTrakula. i did the first step with trac-all -prep -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc This worked properly to the end as shown below: trac-preproc finished without error at Fri Aug 14 17:31:29 CEST 2015 However looking at logfile i found following errors: flirt -in bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/anat/aparc+aseg_mask.nii.gz -ref bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/lowb.nii.gz -out bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dlabel/diff/aparc+aseg_mask.bbr.nii.gz -applyxfm -init bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri/xfms/anat2diff.bbr.mat -interp nearestneighbour terminate called after throwing an instance of 'NEWMAT::SingularException' Abort (core dumped) OR Loading brain mask of output subject from /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz niiRead(): error opening file /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz ERROR: Could not read /home/bm/bmdaten/Auswertung/ALS-Review/Trakula/P01-a/dlabel/mni/lowb_brain_mask.bbr.nii.gz AND as i tried the next step i got the following error: bm@bm-linux:~$ trac-all -bedp -c bmdaten/Auswertung/ALS-Review/Trakula/dmrirc INFO: SUBJECTS_DIR is bmdaten/Auswertung/ALS-Review/Trakula/ INFO: Diffusion root is bmdaten/Auswertung/ALS-Review/Trakula/ Actual FREESURFER_HOME /usr/local/freesurfer WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 bmdaten/Auswertung/ALS-Review/Trakula//P01-a/dmri /usr/local/freesurfer/bin/bedpostx_mgh: 131: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: ( unexpected Could you please advise me what to do? Best Bahram ___ 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.
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
