Re: [Freesurfer] trac-all -path error
Hi Stefano - What are the contents of the bedpostX output directory? In your case, that'd be this directory: /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX a.y On Mon, 11 Feb 2013, std...@virgilio.it wrote: Hi list, I'm running trac-all -path -c $FREESURFER/dmrirc_single_subject but I have this error: Loading mask from /Applications/freesurfer/subjects/subject_prova/Con02/dlabel/diff/aparc+aseg_mask.bbr.nii.gz Loading BEDPOST parameter samples from /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX niiRead(): error opening file /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read /Applications/freesurfer/subjects/subject_prova/Con02/dmri.bedpostX/merged_ph1samples.nii.gz From http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg22066.html I'm deducing that the error may be related trace-all upload. I have doing this upload but I visualize always the same error. I attached tract-all uploades file that live in /Applications/freesurfer/bin. Please, could you check it? I have also other question. May I run the second step of trac-all (bedpostx) using FSL on other pc? In this way, could I directly run in FSL dmri folder? Do you think that I should rename some files? Thanks, Stefano ___ 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] trac-all -path error
Hi Nawaf - Can you please send your trac-all.log? It's possible that the problem started at an earlier step. Thanks, a.y On Thu, 28 Mar 2013, Nawaf Yassi wrote: Dear mailing list I am encountering an error at the trac-all –path stage of a tracula analysis (the first two stages on trac-all seem to have run ok) with the appropriate outputs. I am getting the error “Segmentation fault” (core dumped) very early on after the dmri_paths command is run (see below). Can anyone help? I am using freesurfer 5.2 and FSL 5.0.2.1 (linux) Regards Nawaf ATTACHED: ERROR MESSAGE + config file below = [nyassi@bee1 scripts]$ trac-all -path -c dmrirc_single_subject Too many )'s. INFO: SUBJECTS_DIR is /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer INFO: Diffusion root is /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer Actual FREESURFER_HOME /usr/local/freesurfer5.2 trac-paths -c/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/scripts/ dmrirc.local -log/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/scripts/ trac-all.log -cmd/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/scripts/ trac-all.cmd #- /usr/local/freesurfer5.2/bin/trac-paths #- #@# Path reconstruction Thu Mar 28 10:01:34 EST 2013 rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .cst_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .cst_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .ilf_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .ilf_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .unc_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .unc_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/fm ajor_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/fm inor_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .atr_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .atr_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .ccg_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .ccg_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .cab_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .cab_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .slfp_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .slfp_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .slft_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .slft_PP_avg33_mni_bbr /usr/local/freesurfer5.2/bin/dmri_paths --outdir/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .cst_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .cst_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .ilf_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .ilf_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .unc_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .unc_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/fm ajor_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/fm inor_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .atr_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .atr_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .ccg_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/rh .ccg_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01/dpath/lh .cab_PP_avg33_mni_bbr/bilhome/nyassi/I
Re: [Freesurfer] trac-all -path error
Hi Nawaf - The first error occured much earlier in the log file. Your gradient table file could not be found. Did you set the bvecfile variable in your configuration file? a.y On Fri, 29 Mar 2013, Nawaf Yassi wrote: Hi Anastasia Thanks for your reply Here is the file attached (I have replaced the subject's name with 'A' for anonymity) Regards Nawaf On 29/03/13 2:17 AM, "Anastasia Yendiki" wrote: Hi Nawaf - Can you please send your trac-all.log? It's possible that the problem started at an earlier step. Thanks, a.y On Thu, 28 Mar 2013, Nawaf Yassi wrote: Dear mailing list I am encountering an error at the trac-all path stage of a tracula analysis (the first two stages on trac-all seem to have run ok) with the appropriate outputs. I am getting the error ³Segmentation fault² (core dumped) very early on after the dmri_paths command is run (see below). Can anyone help? I am using freesurfer 5.2 and FSL 5.0.2.1 (linux) Regards Nawaf ATTACHED: ERROR MESSAGE + config file below = [nyassi@bee1 scripts]$ trac-all -path -c dmrirc_single_subject Too many )'s. INFO: SUBJECTS_DIR is /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer INFO: Diffusion root is /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer Actual FREESURFER_HOME /usr/local/freesurfer5.2 trac-paths -c/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 /scripts/ dmrirc.local -log/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C 01/scripts/ trac-all.log -cmd/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C 01/scripts/ trac-all.cmd #- /usr/local/freesurfer5.2/bin/trac-paths #- #@# Path reconstruction Thu Mar 28 10:01:34 EST 2013 rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/lh .cst_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/rh .cst_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/lh .ilf_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/rh .ilf_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/lh .unc_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/rh .unc_AS_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/fm ajor_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/fm inor_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/lh .atr_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/rh .atr_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/lh .ccg_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/rh .ccg_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/lh .cab_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/rh .cab_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/lh .slfp_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/rh .slfp_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/lh .slft_PP_avg33_mni_bbr rm -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 1/dpath/rh .slft_PP_avg33_mni_bbr /usr/local/freesurfer5.2/bin/dmri_paths --outdir/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurf er/C01/dpath/lh .cst_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis /C01_freesurfer/C01/dpath/rh .cst_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis /C01_freesurfer/C01/dpath/lh .ilf_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis /C01_freesurfer/C01/dpath/rh .ilf_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis /C01_freesurfer/C01/dpath/lh .unc_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis /C01_freesurfer/C01/dpath/rh .unc_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis /C01_freesurfer/C01/dpath/fm ajor_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis /C01_freesurfer/C01/dpath/fm inor_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis /C01_freesurfer/C01/dpath/lh .atr_PP_avg33_mni_bbr/bi
Re: [Freesurfer] trac-all -path error
What's in the diff_slices directory? That's a temporary directory that bedpostx creates and that gets deleted after the results get "merged". So my guess would be that bedpostx didn't finish processing. On Fri, 23 Mar 2012, Chris Watson wrote: > Hello, I successfully ran trac-all -bedp, and when I run the next step I > get the following error: > > Loading BEDPOST parameter samples from > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX > niiRead(): error opening file > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz > ERROR: Could not read > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz > Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 > 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux > > trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 > > Word too long. > > > Indeed, the "merged" file doesn't exist. I am running Freesurfer 5.1.0 > and FSL 4.1.9. > Here's what's in the dmri.bedpostX directory: > > [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ > bvals bvecs commands.txt diff_slices logs monitor > nodif_brain_mask.nii.gz xfms > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ 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] trac-all -path error
[freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/ dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz th1samples.nii.gz Come to think of it, when I ran bedpostx, it only output "1 slice processed", but repeated 70 times, or however many slices there are. The data is from a Siemens 3T, by the way. On 03/23/2012 01:16 PM, Anastasia Yendiki wrote: > > What's in the diff_slices directory? That's a temporary directory that > bedpostx creates and that gets deleted after the results get "merged". > So my guess would be that bedpostx didn't finish processing. > > On Fri, 23 Mar 2012, Chris Watson wrote: > >> Hello, I successfully ran trac-all -bedp, and when I run the next step I >> get the following error: >> >> Loading BEDPOST parameter samples from >> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX >> niiRead(): error opening file >> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >> >> >> ERROR: Could not read >> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >> >> >> Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 >> 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux >> >> trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 >> >> Word too long. >> >> >> Indeed, the "merged" file doesn't exist. I am running Freesurfer 5.1.0 >> and FSL 4.1.9. >> Here's what's in the dmri.bedpostX directory: >> >> [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ >> bvals bvecs commands.txt diff_slices logs monitor >> nodif_brain_mask.nii.gz xfms >> >> ___ >> 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
Re: [Freesurfer] trac-all -path error
Oh, ok. That's a known issue, it has to do with changes in the command line of the latest version of bedpostx. We've updated trac-all and it'll be working in our next release but for now you'll have to run bedpostx by itself and not through trac-all. Sorry for the inconvenience! On Fri, 23 Mar 2012, Chris Watson wrote: > [freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/ > dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz > mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz > th1samples.nii.gz > > > Come to think of it, when I ran bedpostx, it only output "1 slice processed", > but repeated 70 times, or however many slices there are. The data is from a > Siemens 3T, by the way. > > On 03/23/2012 01:16 PM, Anastasia Yendiki wrote: >> >> What's in the diff_slices directory? That's a temporary directory that >> bedpostx creates and that gets deleted after the results get "merged". So >> my guess would be that bedpostx didn't finish processing. >> >> On Fri, 23 Mar 2012, Chris Watson wrote: >> >> > Hello, I successfully ran trac-all -bedp, and when I run the next step I >> > get the following error: >> > >> > Loading BEDPOST parameter samples from >> > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX >> > niiRead(): error opening file >> > >> > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >> > >> > >> > ERROR: Could not read >> > >> > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >> > >> > >> > Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 >> > 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux >> > >> > trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 >> > >> > Word too long. >> > >> > >> > Indeed, the "merged" file doesn't exist. I am running Freesurfer 5.1.0 >> > and FSL 4.1.9. >> > Here's what's in the dmri.bedpostX directory: >> > >> > [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ >> > bvals bvecs commands.txt diff_slices logs monitor >> > nodif_brain_mask.nii.gz xfms >> > >> > ___ >> > 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
Re: [Freesurfer] trac-all -path error
Ok. Do I run it with the defaults? # fibers per voxel = 2 ARD weight = 1 burn-in period = 1000 # jumps = 1250 sample every = 25 On 03/23/2012 01:22 PM, Anastasia Yendiki wrote: > > Oh, ok. That's a known issue, it has to do with changes in the command > line of the latest version of bedpostx. We've updated trac-all and > it'll be working in our next release but for now you'll have to run > bedpostx by itself and not through trac-all. Sorry for the inconvenience! > > On Fri, 23 Mar 2012, Chris Watson wrote: > >> [freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/ >> dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz >> mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz >> th1samples.nii.gz >> >> >> Come to think of it, when I ran bedpostx, it only output "1 slice >> processed", but repeated 70 times, or however many slices there are. >> The data is from a Siemens 3T, by the way. >> >> On 03/23/2012 01:16 PM, Anastasia Yendiki wrote: >>> >>> What's in the diff_slices directory? That's a temporary directory that >>> bedpostx creates and that gets deleted after the results get >>> "merged". So >>> my guess would be that bedpostx didn't finish processing. >>> >>> On Fri, 23 Mar 2012, Chris Watson wrote: >>> >>> > Hello, I successfully ran trac-all -bedp, and when I run the next >>> step I >>> > get the following error: >>> > > Loading BEDPOST parameter samples from >>> > >>> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX >>> > niiRead(): error opening file >>> > >>> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >>> >>> > > ERROR: Could not read >>> > >>> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >>> >>> > > Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed >>> Mar 7 >>> > 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux >>> > > trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 >>> > > Word too long. >>> > >>> >>> >>> > > Indeed, the "merged" file doesn't exist. I am running >>> Freesurfer 5.1.0 >>> > and FSL 4.1.9. >>> > Here's what's in the dmri.bedpostX directory: >>> > > [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ >>> > bvals bvecs commands.txt diff_slices logs monitor >>> > nodif_brain_mask.nii.gz xfms >>> > > ___ >>> > 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
Re: [Freesurfer] trac-all -path error
Yes. On Fri, 23 Mar 2012, Chris Watson wrote: > Ok. Do I run it with the defaults? > # fibers per voxel = 2 > ARD weight = 1 > burn-in period = 1000 > # jumps = 1250 > sample every = 25 > > On 03/23/2012 01:22 PM, Anastasia Yendiki wrote: >> >> Oh, ok. That's a known issue, it has to do with changes in the command >> line of the latest version of bedpostx. We've updated trac-all and it'll >> be working in our next release but for now you'll have to run bedpostx by >> itself and not through trac-all. Sorry for the inconvenience! >> >> On Fri, 23 Mar 2012, Chris Watson wrote: >> >> > [freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/ >> > dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz >> > mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz >> > th1samples.nii.gz >> > >> > >> > Come to think of it, when I ran bedpostx, it only output "1 slice >> > processed", but repeated 70 times, or however many slices there are. The >> > data is from a Siemens 3T, by the way. >> > >> > On 03/23/2012 01:16 PM, Anastasia Yendiki wrote: >> > > >> > > What's in the diff_slices directory? That's a temporary directory >> > > that >> > > bedpostx creates and that gets deleted after the results get >> > > "merged". So >> > > my guess would be that bedpostx didn't finish processing. >> > > >> > > On Fri, 23 Mar 2012, Chris Watson wrote: >> > > >> > > > Hello, I successfully ran trac-all -bedp, and when I run the next >> > > step I >> > > > get the following error: >> > > > > Loading BEDPOST parameter samples from >> > > > >> > > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX >> > > > niiRead(): error opening file >> > > > >> > > >> > > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >> > > >> > > > > ERROR: Could not read >> > > > >> > > >> > > /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz >> > > >> > > > > Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed >> > > Mar 7 >> > > > 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux >> > > > > trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 >> > > > > Word too long. >> > > > >> > > >> > > >> > > >> > > > > Indeed, the "merged" file doesn't exist. I am running >> > > Freesurfer 5.1.0 >> > > > and FSL 4.1.9. >> > > > Here's what's in the dmri.bedpostX directory: >> > > > > [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ >> > > > bvals bvecs commands.txt diff_slices logs monitor >> > > > nodif_brain_mask.nii.gz xfms >> > > > > ___ >> > > > 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
Re: [Freesurfer] trac-all -path error
Hi, I'm getting the same error as before; "merged_ph1samples.nii.gz" isn't getting created, I think. This is after I ran bedpostx on its own, per your instructions from this thread. Here are the last few lines of output from trac-all -path: Loading BEDPOST parameter samples from /raid2/fmri8/control/H008B/dmri.bedpostX niiRead(): error opening file /raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read /raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz /parietal/freesurfer/current/bin/dmri_mergepaths --indir /raid2/fmri8/control/H008B/dpath --in --out /raid2/fmri8/control/H008B/dpath/merged_avg33_mni_bbr.mgz --ctab /parietal/freesurfer/current/FreeSurferColorLUT.txt --thresh .15 ERROR: must specify input volume(s) This is what's in "dmri.bedpostX": bvals diff_slices logs mean_ph2samples.nii.gz merged_f2samples.nii.gz monitor bvecs dyads2_dispersion.nii.gz mean_dsamples.nii.gz mean_S0samples.nii.gz merged_ph2samples.nii.gz nodif_brain_mask.nii.gz commands.txt dyads2.nii.gz mean_f2samples.nii.gz mean_th2samples.nii.gz merged_th2samples.nii.gz xfms Thanks, Chris On 03/23/2012 01:25 PM, Anastasia Yendiki wrote: Yes. On Fri, 23 Mar 2012, Chris Watson wrote: Ok. Do I run it with the defaults? # fibers per voxel = 2 ARD weight = 1 burn-in period = 1000 # jumps = 1250 sample every = 25 On 03/23/2012 01:22 PM, Anastasia Yendiki wrote: Oh, ok. That's a known issue, it has to do with changes in the command line of the latest version of bedpostx. We've updated trac-all and it'll be working in our next release but for now you'll have to run bedpostx by itself and not through trac-all. Sorry for the inconvenience! On Fri, 23 Mar 2012, Chris Watson wrote: [freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/ dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz th1samples.nii.gz Come to think of it, when I ran bedpostx, it only output "1 slice processed", but repeated 70 times, or however many slices there are. The data is from a Siemens 3T, by the way. On 03/23/2012 01:16 PM, Anastasia Yendiki wrote: What's in the diff_slices directory? That's a temporary directory that bedpostx creates and that gets deleted after the results get "merged". So my guess would be that bedpostx didn't finish processing. On Fri, 23 Mar 2012, Chris Watson wrote: Hello, I successfully ran trac-all -bedp, and when I run the next step I get the following error: Loading BEDPOST parameter samples from /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX niiRead(): error opening file /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 Word too long. Indeed, the "merged" file doesn't exist. I am running Freesurfer 5.1.0 and FSL 4.1.9. Here's what's in the dmri.bedpostX directory: [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ bvals bvecs commands.txt diff_slices logs monitor nodif_brain_mask.nii.gz xfms ___ 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 ___ 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, pl
Re: [Freesurfer] trac-all -path error
Hi Chris, The diff_slices folder is still there, which means that bedpostX probably did not finish processing. That folder usually gets deleted after bedpostX processing completes. It's strange that you have merged_ph2samples.nii.gz and not merged_ph1samples.nii.gz. Did you accidentally run bedpostX twice and exit out of it in the middle? It is quite possible that you'd already finished processing bedpostX(and all files were properly created) and started running it again, which would explain the diff_slices and the absence of merged_ph1samples (but not merged_ph2samples). You could potentially back up your current bedpostx folder and re-run bedpostX to see if that solves your issue. Could you also send the commandline you're using for bedpostX? Thanks, Priti > Hi, I'm getting the same error as before; "merged_ph1samples.nii.gz" > isn't getting created, I think. This is after I ran bedpostx on its own, > per your instructions from this thread. > > Here are the last few lines of output from trac-all -path: > Loading BEDPOST parameter samples from > /raid2/fmri8/control/H008B/dmri.bedpostX > niiRead(): error opening file > /raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz > ERROR: Could not read > /raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz > /parietal/freesurfer/current/bin/dmri_mergepaths --indir > /raid2/fmri8/control/H008B/dpath --in --out > /raid2/fmri8/control/H008B/dpath/merged_avg33_mni_bbr.mgz --ctab > /parietal/freesurfer/current/FreeSurferColorLUT.txt --thresh .15 > ERROR: must specify input volume(s) > > This is what's in "dmri.bedpostX": > bvals diff_slices logs > mean_ph2samples.nii.gz merged_f2samples.nii.gz monitor > bvecs dyads2_dispersion.nii.gz mean_dsamples.nii.gz > mean_S0samples.nii.gz merged_ph2samples.nii.gz > nodif_brain_mask.nii.gz > commands.txt dyads2.nii.gz mean_f2samples.nii.gz > mean_th2samples.nii.gz merged_th2samples.nii.gz xfms > > Thanks, > Chris > > On 03/23/2012 01:25 PM, Anastasia Yendiki wrote: >> Yes. >> >> On Fri, 23 Mar 2012, Chris Watson wrote: >> >>> Ok. Do I run it with the defaults? >>> # fibers per voxel = 2 >>> ARD weight = 1 >>> burn-in period = 1000 >>> # jumps = 1250 >>> sample every = 25 >>> >>> On 03/23/2012 01:22 PM, Anastasia Yendiki wrote: Oh, ok. That's a known issue, it has to do with changes in the command line of the latest version of bedpostx. We've updated trac-all and it'll be working in our next release but for now you'll have to run bedpostx by itself and not through trac-all. Sorry for the inconvenience! On Fri, 23 Mar 2012, Chris Watson wrote: > [freesurfer@occipital dmri.bedpostX]$ ls > diff_slices/data_slice_0002/ > dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz > mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz > th1samples.nii.gz > > > Come to think of it, when I ran bedpostx, it only output "1 slice > processed", but repeated 70 times, or however many slices there > are. The > data is from a Siemens 3T, by the way. > > On 03/23/2012 01:16 PM, Anastasia Yendiki wrote: >>What's in the diff_slices directory? That's a temporary directory >>that >>bedpostx creates and that gets deleted after the results get >> "merged". So >>my guess would be that bedpostx didn't finish processing. >> >>On Fri, 23 Mar 2012, Chris Watson wrote: >> >>>Hello, I successfully ran trac-all -bedp, and when I run the >>> next >> step I >>>get the following error: Loading BEDPOST parameter samples from >> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX >>>niiRead(): error opening file >>> >> >> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read >> >> /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed >> Mar 7 >>>04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 Word too long. >> >> >> Indeed, the "merged" file doesn't exist. I am running >> Freesurfer 5.1.0 >>>and FSL 4.1.9. >>>Here's what's in the dmri.bedpostX directory: [freesurfer@occipital control]$ ls murphy_p/dmri.bedpostX/ >>>bvals bvecs commands.txt diff_slices logs monitor >>>nodif_brain_mask.nii.gz xfms ___ >>>Freesurfer mailing list >>>Freesurfer@nmr.mgh.harvard.edu >
Re: [Freesurfer] trac-all -path error
Yes, I figured out that I had previously run "trac-all -bedp" and it created "data_slice_0002". I deleted this directory, and bedpostx finished, but now I get this error from "trac-all-path": Segmentation fault (core dumped) /parietal/freesurfer/current/bin/dmri_mergepaths --indir /raid2/fmri8/control/H008B/dpath --in --out /raid2/fmri8/control/H008B/dpath/merged_avg33_mni_bbr.mgz --ctab /parietal/freesurfer/current/FreeSurferColorLUT.txt --thresh .15 ERROR: must specify input volume(s) What should be specified here? Thanks, Chris PS When running bedpostx I was simply using the defaults, so "bedpostx H008B/dmri.bedpostX" was the command line. On 05/07/2012 02:28 PM, Priti Srinivasan wrote: Hi Chris, The diff_slices folder is still there, which means that bedpostX probably did not finish processing. That folder usually gets deleted after bedpostX processing completes. It's strange that you have merged_ph2samples.nii.gz and not merged_ph1samples.nii.gz. Did you accidentally run bedpostX twice and exit out of it in the middle? It is quite possible that you'd already finished processing bedpostX(and all files were properly created) and started running it again, which would explain the diff_slices and the absence of merged_ph1samples (but not merged_ph2samples). You could potentially back up your current bedpostx folder and re-run bedpostX to see if that solves your issue. Could you also send the commandline you're using for bedpostX? Thanks, Priti Hi, I'm getting the same error as before; "merged_ph1samples.nii.gz" isn't getting created, I think. This is after I ran bedpostx on its own, per your instructions from this thread. Here are the last few lines of output from trac-all -path: Loading BEDPOST parameter samples from /raid2/fmri8/control/H008B/dmri.bedpostX niiRead(): error opening file /raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read /raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz /parietal/freesurfer/current/bin/dmri_mergepaths --indir /raid2/fmri8/control/H008B/dpath --in --out /raid2/fmri8/control/H008B/dpath/merged_avg33_mni_bbr.mgz --ctab /parietal/freesurfer/current/FreeSurferColorLUT.txt --thresh .15 ERROR: must specify input volume(s) This is what's in "dmri.bedpostX": bvals diff_slices logs mean_ph2samples.nii.gz merged_f2samples.nii.gz monitor bvecs dyads2_dispersion.nii.gz mean_dsamples.nii.gz mean_S0samples.nii.gz merged_ph2samples.nii.gz nodif_brain_mask.nii.gz commands.txt dyads2.nii.gz mean_f2samples.nii.gz mean_th2samples.nii.gz merged_th2samples.nii.gz xfms Thanks, Chris On 03/23/2012 01:25 PM, Anastasia Yendiki wrote: Yes. On Fri, 23 Mar 2012, Chris Watson wrote: Ok. Do I run it with the defaults? # fibers per voxel = 2 ARD weight = 1 burn-in period = 1000 # jumps = 1250 sample every = 25 On 03/23/2012 01:22 PM, Anastasia Yendiki wrote: Oh, ok. That's a known issue, it has to do with changes in the command line of the latest version of bedpostx. We've updated trac-all and it'll be working in our next release but for now you'll have to run bedpostx by itself and not through trac-all. Sorry for the inconvenience! On Fri, 23 Mar 2012, Chris Watson wrote: [freesurfer@occipital dmri.bedpostX]$ ls diff_slices/data_slice_0002/ dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz th1samples.nii.gz Come to think of it, when I ran bedpostx, it only output "1 slice processed", but repeated 70 times, or however many slices there are. The data is from a Siemens 3T, by the way. On 03/23/2012 01:16 PM, Anastasia Yendiki wrote: What's in the diff_slices directory? That's a temporary directory that bedpostx creates and that gets deleted after the results get "merged". So my guess would be that bedpostx didn't finish processing. On Fri, 23 Mar 2012, Chris Watson wrote: Hello, I successfully ran trac-all -bedp, and when I run the next step I get the following error: Loading BEDPOST parameter samples from /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX niiRead(): error opening file /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz ERROR: Could not read /raid2/fmri8/study/volumetric/freesurfer/control/subject/dmri.bedpostX/merged_ph1samples.nii.gz Linux occipital.tch.harvard.edu 2.6.18-308.1.1.el5 #1 SMP Wed Mar 7 04:16:51 EST 2012 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at Fri Mar 23 11:24:11 EDT 2012 Word too long. Indeed, the "merged" file doesn't exist. I am running Freesurfer 5.1.0 and FSL 4.1.9. Here's what's in the dmri.bedpostX directory: [freesurf
Re: [Freesurfer] trac-all -path error
So I'm assuming that you don't have any issues merged_ph* files anymore? As far as the error below is concerned, this is typically the last step in trac-paths, where it should merge all the 18 tracts to create a 4D tract volume for visualization. The input for this should be all the 18 posterior distribution volumes. From what I see below, it does not look like the tract reconstruction finished for any of the tracts (which is why --in is empty). If you send us the trac-all.log, I can take a look. Also do you see any tract volumes under dpath/ ? Hope that helps, Priti > Yes, I figured out that I had previously run "trac-all -bedp" and it > created "data_slice_0002". I deleted this directory, and bedpostx > finished, but now I get this error from "trac-all-path": > Segmentation fault (core dumped) > /parietal/freesurfer/current/bin/dmri_mergepaths --indir > /raid2/fmri8/control/H008B/dpath --in --out > /raid2/fmri8/control/H008B/dpath/merged_avg33_mni_bbr.mgz --ctab > /parietal/freesurfer/current/FreeSurferColorLUT.txt --thresh .15 > ERROR: must specify input volume(s) > > What should be specified here? > > Thanks, > Chris > > PS When running bedpostx I was simply using the defaults, so "bedpostx > H008B/dmri.bedpostX" was the command line. > > On 05/07/2012 02:28 PM, Priti Srinivasan wrote: >> Hi Chris, >> >> The diff_slices folder is still there, which means that bedpostX >> probably >> did not finish processing. That folder usually gets deleted after >> bedpostX >> processing completes. It's strange that you have >> merged_ph2samples.nii.gz >> and not merged_ph1samples.nii.gz. >> >> Did you accidentally run bedpostX twice and exit out of it in the >> middle? >> It is quite possible that you'd already finished processing bedpostX(and >> all files were properly created) and started running it again, which >> would >> explain the diff_slices and the absence of merged_ph1samples (but not >> merged_ph2samples). >> >> You could potentially back up your current bedpostx folder and re-run >> bedpostX to see if that solves your issue. >> >> Could you also send the commandline you're using for bedpostX? >> >> Thanks, >> Priti >> >>> Hi, I'm getting the same error as before; "merged_ph1samples.nii.gz" >>> isn't getting created, I think. This is after I ran bedpostx on its >>> own, >>> per your instructions from this thread. >>> >>> Here are the last few lines of output from trac-all -path: >>> Loading BEDPOST parameter samples from >>> /raid2/fmri8/control/H008B/dmri.bedpostX >>> niiRead(): error opening file >>> /raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz >>> ERROR: Could not read >>> /raid2/fmri8/control/H008B/dmri.bedpostX/merged_ph1samples.nii.gz >>> /parietal/freesurfer/current/bin/dmri_mergepaths --indir >>> /raid2/fmri8/control/H008B/dpath --in --out >>> /raid2/fmri8/control/H008B/dpath/merged_avg33_mni_bbr.mgz --ctab >>> /parietal/freesurfer/current/FreeSurferColorLUT.txt --thresh .15 >>> ERROR: must specify input volume(s) >>> >>> This is what's in "dmri.bedpostX": >>> bvals diff_slices logs >>> mean_ph2samples.nii.gz merged_f2samples.nii.gz monitor >>> bvecs dyads2_dispersion.nii.gz mean_dsamples.nii.gz >>> mean_S0samples.nii.gz merged_ph2samples.nii.gz >>> nodif_brain_mask.nii.gz >>> commands.txt dyads2.nii.gz mean_f2samples.nii.gz >>> mean_th2samples.nii.gz merged_th2samples.nii.gz xfms >>> >>> Thanks, >>> Chris >>> >>> On 03/23/2012 01:25 PM, Anastasia Yendiki wrote: Yes. On Fri, 23 Mar 2012, Chris Watson wrote: > Ok. Do I run it with the defaults? > # fibers per voxel = 2 > ARD weight = 1 > burn-in period = 1000 > # jumps = 1250 > sample every = 25 > > On 03/23/2012 01:22 PM, Anastasia Yendiki wrote: >>Oh, ok. That's a known issue, it has to do with changes in the >> command >>line of the latest version of bedpostx. We've updated trac-all >> and >> it'll >>be working in our next release but for now you'll have to run >> bedpostx by >>itself and not through trac-all. Sorry for the inconvenience! >> >>On Fri, 23 Mar 2012, Chris Watson wrote: >> >>>[freesurfer@occipital dmri.bedpostX]$ ls >>> diff_slices/data_slice_0002/ >>>dyads1.nii.gz f1samples.nii.gz logfile mean_dsamples.nii.gz >>>mean_f1samples.nii.gz mean_S0samples.nii.gz ph1samples.nii.gz >>>th1samples.nii.gz >>> >>> >>>Come to think of it, when I ran bedpostx, it only output "1 >>> slice >>>processed", but repeated 70 times, or however many slices there >>> are. The >>>data is from a Siemens 3T, by the way. >>> >>>On 03/23/2012 01:16 PM, Anastasia Yendiki wrote: What's in the diff_slices directory? That's a temporary directory that bedpostx creates and that gets deleted after the results get
Re: [Freesurfer] trac-all -path error
Hi Kiely, Have you checked your inter and intra subject registrations? The control points going off the dwi is not only for one paths but for all the paths. If the registration goes terribly wrong, this can happen. You can take a look at /dmri/lowb_brain_anat.flt.nii.gz (For intra subject registration diff-anat) and /dmri/brain_anat_mni.nii.gz (For inter-subject registration anat-mni) I would start by checking that first. Priti > Hello-- > > I have run Tracula successfully for ~75 healthy subjects. However, the > pathway reconstruction seems to fail for a handful of people. I've > attached > the log file for one of these subjects. It appears that the control points > are not within the dwi. A similar problem occurred in a subject with > substantial signal loss in the dwi, but that doesn't seem to be the case > for this particular person. I have been creating the entire set of tracts, > but at this point, I'm only interested in the SLFt and SLFp. > > Thanks, > > Kiely > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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] trac-all -path error
Hi Priti - Thanks for your help. The inter-subject registration seems to have run OK, but there must be something wrong with the intra-subject registration. When I try to view it using freeview, it's completely dark - I don't see a brain at all. Is there a way to troubleshoot this? Thanks, Kiely On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan < rspr...@nmr.mgh.harvard.edu> wrote: > Hi Kiely, > > Have you checked your inter and intra subject registrations? The control > points going off the dwi is not only for one paths but for all the paths. > If the registration goes terribly wrong, this can happen. You can take a > look at > > /dmri/lowb_brain_anat.flt.nii.gz (For intra subject registration diff-anat) > > and > > /dmri/brain_anat_mni.nii.gz (For inter-subject registration anat-mni) > > I would start by checking that first. > > Priti > > > Hello-- > > > > I have run Tracula successfully for ~75 healthy subjects. However, the > > pathway reconstruction seems to fail for a handful of people. I've > > attached > > the log file for one of these subjects. It appears that the control > points > > are not within the dwi. A similar problem occurred in a subject with > > substantial signal loss in the dwi, but that doesn't seem to be the case > > for this particular person. I have been creating the entire set of > tracts, > > but at this point, I'm only interested in the SLFt and SLFp. > > > > Thanks, > > > > Kiely > > ___ > > 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. > > -- Kiely M. Donnelly, M.A. Doctoral Candidate, Clinical Neuropsychology University of Cincinnati ___ 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] trac-all -path error
Hi Kiely - Looks like you used flirt for the intra-subject registration, so you can look in trac-all.log for the flirt command line that registers diffusion to anatomical and play around with the parameters. You can also use bbregister instead of flirt for the intra-subject registration - it has the option to initialize with flirt or with SPM. Hope this helps, a.y On Wed, 16 May 2012, Kiely Donnelly wrote: Hi Priti - Thanks for your help. The inter-subject registration seems to have run OK, but there must be something wrong with the intra-subject registration. When I try to view it using freeview, it's completely dark - I don't see a brain at all. Is there a way to troubleshoot this? Thanks, Kiely On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan wrote: Hi Kiely, Have you checked your inter and intra subject registrations? The control points going off the dwi is not only for one paths but for all the paths. If the registration goes terribly wrong, this can happen. You can take a look at /dmri/lowb_brain_anat.flt.nii.gz (For intra subject registration diff-anat) and /dmri/brain_anat_mni.nii.gz (For inter-subject registration anat-mni) I would start by checking that first. Priti > Hello-- > > I have run Tracula successfully for ~75 healthy subjects. However, the > pathway reconstruction seems to fail for a handful of people. I've > attached > the log file for one of these subjects. It appears that the control points > are not within the dwi. A similar problem occurred in a subject with > substantial signal loss in the dwi, but that doesn't seem to be the case > for this particular person. I have been creating the entire set of tracts, > but at this point, I'm only interested in the SLFt and SLFp. > > Thanks, > > Kiely > ___ > 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. -- Kiely M. Donnelly, M.A. Doctoral Candidate, Clinical Neuropsychology University of Cincinnati ___ 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] trac-all -path error
Kiely, For flirt, try using corratio, cost function instead of mutualinfo (which is the default in trac-all) to see if that solves your registration problem. > Hi Kiely - Looks like you used flirt for the intra-subject registration, > so you can look in trac-all.log for the flirt command line that registers > diffusion to anatomical and play around with the parameters. > > You can also use bbregister instead of flirt for the intra-subject > registration - it has the option to initialize with flirt or with SPM. > > Hope this helps, > a.y > > On Wed, 16 May 2012, Kiely Donnelly wrote: > >> Hi Priti - Thanks for your help. The inter-subject registration seems to >> have run OK, but there must be something wrong with the intra-subject >> registration. When I try to view it using freeview, it's completely dark >> - I >> don't see a brain at all. Is there a way to troubleshoot this? >> Thanks, >> >> Kiely >> >> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan >> wrote: >> Hi Kiely, >> >> Have you checked your inter and intra subject registrations? The >> control >> points going off the dwi is not only for one paths but for all >> the paths. >> If the registration goes terribly wrong, this can happen. You >> can take a >> look at >> >> /dmri/lowb_brain_anat.flt.nii.gz (For intra subject registration >> diff-anat) >> >> and >> >> /dmri/brain_anat_mni.nii.gz (For inter-subject registration >> anat-mni) >> >> I would start by checking that first. >> >> Priti >> >> > Hello-- >> > >> > I have run Tracula successfully for ~75 healthy subjects. >> However, the >> > pathway reconstruction seems to fail for a handful of people. >> I've >> > attached >> > the log file for one of these subjects. It appears that the >> control points >> > are not within the dwi. A similar problem occurred in a >> subject with >> > substantial signal loss in the dwi, but that doesn't seem to >> be the case >> > for this particular person. I have been creating the entire >> set of tracts, >> > but at this point, I'm only interested in the SLFt and SLFp. >> > >> > Thanks, >> > >> > Kiely >> > ___ >> > 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. >> >> >> >> >> -- >> Kiely M. Donnelly, M.A. >> Doctoral Candidate, Clinical Neuropsychology >> University of Cincinnati >> >>___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] trac-all -path error
Is this something I can change in my dmrirc file or do I need to run flirt on it's own? Thanks, Kiely On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan < rspr...@nmr.mgh.harvard.edu> wrote: > Kiely, For flirt, try using corratio, cost function instead of mutualinfo > (which is the default in trac-all) to see if that solves your registration > problem. > > > > Hi Kiely - Looks like you used flirt for the intra-subject registration, > > so you can look in trac-all.log for the flirt command line that registers > > diffusion to anatomical and play around with the parameters. > > > > You can also use bbregister instead of flirt for the intra-subject > > registration - it has the option to initialize with flirt or with SPM. > > > > Hope this helps, > > a.y > > > > On Wed, 16 May 2012, Kiely Donnelly wrote: > > > >> Hi Priti - Thanks for your help. The inter-subject registration seems to > >> have run OK, but there must be something wrong with the intra-subject > >> registration. When I try to view it using freeview, it's completely dark > >> - I > >> don't see a brain at all. Is there a way to troubleshoot this? > >> Thanks, > >> > >> Kiely > >> > >> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan > >> wrote: > >> Hi Kiely, > >> > >> Have you checked your inter and intra subject registrations? The > >> control > >> points going off the dwi is not only for one paths but for all > >> the paths. > >> If the registration goes terribly wrong, this can happen. You > >> can take a > >> look at > >> > >> /dmri/lowb_brain_anat.flt.nii.gz (For intra subject registration > >> diff-anat) > >> > >> and > >> > >> /dmri/brain_anat_mni.nii.gz (For inter-subject registration > >> anat-mni) > >> > >> I would start by checking that first. > >> > >> Priti > >> > >> > Hello-- > >> > > >> > I have run Tracula successfully for ~75 healthy subjects. > >> However, the > >> > pathway reconstruction seems to fail for a handful of people. > >> I've > >> > attached > >> > the log file for one of these subjects. It appears that the > >> control points > >> > are not within the dwi. A similar problem occurred in a > >> subject with > >> > substantial signal loss in the dwi, but that doesn't seem to > >> be the case > >> > for this particular person. I have been creating the entire > >> set of tracts, > >> > but at this point, I'm only interested in the SLFt and SLFp. > >> > > >> > Thanks, > >> > > >> > Kiely > >> > ___ > >> > 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. > >> > >> > >> > >> > >> -- > >> Kiely M. Donnelly, M.A. > >> Doctoral Candidate, Clinical Neuropsychology > >> University of Cincinnati > >> > >>___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Kiely M. Donnelly, M.A. Doctoral Candidate, Clinical Neuropsychology University of Cincinnati ___ 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] trac-all -path error
No, this is something you have to try yourself on the command line. If you want to make the change permanent, you can edit the relevant line in $FREESURFER_HOME/bin/trac-preproc. On Wed, 16 May 2012, Kiely Donnelly wrote: Is this something I can change in my dmrirc file or do I need to run flirt on it's own? Thanks, Kiely On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan wrote: Kiely, For flirt, try using corratio, cost function instead of mutualinfo (which is the default in trac-all) to see if that solves your registration problem. > Hi Kiely - Looks like you used flirt for the intra-subject registration, > so you can look in trac-all.log for the flirt command line that registers > diffusion to anatomical and play around with the parameters. > > You can also use bbregister instead of flirt for the intra-subject > registration - it has the option to initialize with flirt or with SPM. > > Hope this helps, > a.y > > On Wed, 16 May 2012, Kiely Donnelly wrote: > >> Hi Priti - Thanks for your help. The inter-subject registration seems to >> have run OK, but there must be something wrong with the intra-subject >> registration. When I try to view it using freeview, it's completely dark >> - I >> don't see a brain at all. Is there a way to troubleshoot this? >> Thanks, >> >> Kiely >> >> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan >> wrote: >> Hi Kiely, >> >> Have you checked your inter and intra subject registrations? The >> control >> points going off the dwi is not only for one paths but for all >> the paths. >> If the registration goes terribly wrong, this can happen. You >> can take a >> look at >> >> /dmri/lowb_brain_anat.flt.nii.gz (For intra subject registration >> diff-anat) >> >> and >> >> /dmri/brain_anat_mni.nii.gz (For inter-subject registration >> anat-mni) >> >> I would start by checking that first. >> >> Priti >> >> > Hello-- >> > >> > I have run Tracula successfully for ~75 healthy subjects. >> However, the >> > pathway reconstruction seems to fail for a handful of people. >> I've >> > attached >> > the log file for one of these subjects. It appears that the >> control points >> > are not within the dwi. A similar problem occurred in a >> subject with >> > substantial signal loss in the dwi, but that doesn't seem to >> be the case >> > for this particular person. I have been creating the entire >> set of tracts, >> > but at this point, I'm only interested in the SLFt and SLFp. >> > >> > Thanks, >> > >> > Kiely >> > ___ >> > 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. >> >> >> >> >> -- >> Kiely M. Donnelly, M.A. >> Doctoral Candidate, Clinical Neuropsychology >> University of Cincinnati >> >>___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kiely M. Donnelly, M.A. Doctoral Candidate, Clinical Neuropsychology University of Cincinnati ___ 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 contai
Re: [Freesurfer] trac-all -path error
you have to run flirt commandline separately to check if it solves your problem. > Is this something I can change in my dmrirc file or do I need to run flirt > on it's own? > > Thanks, > > Kiely > > On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan < > rspr...@nmr.mgh.harvard.edu> wrote: > >> Kiely, For flirt, try using corratio, cost function instead of >> mutualinfo >> (which is the default in trac-all) to see if that solves your >> registration >> problem. >> >> >> > Hi Kiely - Looks like you used flirt for the intra-subject >> registration, >> > so you can look in trac-all.log for the flirt command line that >> registers >> > diffusion to anatomical and play around with the parameters. >> > >> > You can also use bbregister instead of flirt for the intra-subject >> > registration - it has the option to initialize with flirt or with SPM. >> > >> > Hope this helps, >> > a.y >> > >> > On Wed, 16 May 2012, Kiely Donnelly wrote: >> > >> >> Hi Priti - Thanks for your help. The inter-subject registration seems >> to >> >> have run OK, but there must be something wrong with the intra-subject >> >> registration. When I try to view it using freeview, it's completely >> dark >> >> - I >> >> don't see a brain at all. Is there a way to troubleshoot this? >> >> Thanks, >> >> >> >> Kiely >> >> >> >> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan >> >> wrote: >> >> Hi Kiely, >> >> >> >> Have you checked your inter and intra subject registrations? >> The >> >> control >> >> points going off the dwi is not only for one paths but for all >> >> the paths. >> >> If the registration goes terribly wrong, this can happen. You >> >> can take a >> >> look at >> >> >> >> /dmri/lowb_brain_anat.flt.nii.gz (For intra subject >> registration >> >> diff-anat) >> >> >> >> and >> >> >> >> /dmri/brain_anat_mni.nii.gz (For inter-subject registration >> >> anat-mni) >> >> >> >> I would start by checking that first. >> >> >> >> Priti >> >> >> >> > Hello-- >> >> > >> >> > I have run Tracula successfully for ~75 healthy subjects. >> >> However, the >> >> > pathway reconstruction seems to fail for a handful of people. >> >> I've >> >> > attached >> >> > the log file for one of these subjects. It appears that the >> >> control points >> >> > are not within the dwi. A similar problem occurred in a >> >> subject with >> >> > substantial signal loss in the dwi, but that doesn't seem to >> >> be the case >> >> > for this particular person. I have been creating the entire >> >> set of tracts, >> >> > but at this point, I'm only interested in the SLFt and SLFp. >> >> > >> >> > Thanks, >> >> > >> >> > Kiely >> >> > ___ >> >> > 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. >> >> >> >> >> >> >> >> >> >> -- >> >> Kiely M. Donnelly, M.A. >> >> Doctoral Candidate, Clinical Neuropsychology >> >> University of Cincinnati >> >> >> >>___ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> > > > -- > Kiely M. Donnelly, M.A. > Doctoral Candidate, Clinical Neuropsychology > University of Cincinnati > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] trac-all -path error
I tried using corratio and it seems to have fixed the registration issue. I'm very new to this so just want to make sure I did it correctly before I move forward. Should the command line look something like this if I am running it in this individuals dmri directory: flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz -out lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat -cost corratio Thanks so much for your help. Kiely On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan < rspr...@nmr.mgh.harvard.edu> wrote: > you have to run flirt commandline separately to check if it solves your > problem. > > > > Is this something I can change in my dmrirc file or do I need to run > flirt > > on it's own? > > > > Thanks, > > > > Kiely > > > > On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan < > > rspr...@nmr.mgh.harvard.edu> wrote: > > > >> Kiely, For flirt, try using corratio, cost function instead of > >> mutualinfo > >> (which is the default in trac-all) to see if that solves your > >> registration > >> problem. > >> > >> > >> > Hi Kiely - Looks like you used flirt for the intra-subject > >> registration, > >> > so you can look in trac-all.log for the flirt command line that > >> registers > >> > diffusion to anatomical and play around with the parameters. > >> > > >> > You can also use bbregister instead of flirt for the intra-subject > >> > registration - it has the option to initialize with flirt or with SPM. > >> > > >> > Hope this helps, > >> > a.y > >> > > >> > On Wed, 16 May 2012, Kiely Donnelly wrote: > >> > > >> >> Hi Priti - Thanks for your help. The inter-subject registration seems > >> to > >> >> have run OK, but there must be something wrong with the intra-subject > >> >> registration. When I try to view it using freeview, it's completely > >> dark > >> >> - I > >> >> don't see a brain at all. Is there a way to troubleshoot this? > >> >> Thanks, > >> >> > >> >> Kiely > >> >> > >> >> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan > >> >> wrote: > >> >> Hi Kiely, > >> >> > >> >> Have you checked your inter and intra subject registrations? > >> The > >> >> control > >> >> points going off the dwi is not only for one paths but for all > >> >> the paths. > >> >> If the registration goes terribly wrong, this can happen. You > >> >> can take a > >> >> look at > >> >> > >> >> /dmri/lowb_brain_anat.flt.nii.gz (For intra subject > >> registration > >> >> diff-anat) > >> >> > >> >> and > >> >> > >> >> /dmri/brain_anat_mni.nii.gz (For inter-subject registration > >> >> anat-mni) > >> >> > >> >> I would start by checking that first. > >> >> > >> >> Priti > >> >> > >> >> > Hello-- > >> >> > > >> >> > I have run Tracula successfully for ~75 healthy subjects. > >> >> However, the > >> >> > pathway reconstruction seems to fail for a handful of people. > >> >> I've > >> >> > attached > >> >> > the log file for one of these subjects. It appears that the > >> >> control points > >> >> > are not within the dwi. A similar problem occurred in a > >> >> subject with > >> >> > substantial signal loss in the dwi, but that doesn't seem to > >> >> be the case > >> >> > for this particular person. I have been creating the entire > >> >> set of tracts, > >> >> > but at this point, I'm only interested in the SLFt and SLFp. > >> >> > > >> >> > Thanks, > >> >> > > >> >> > Kiely > >> >> > ___ > >> >> > 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. > >> >> > >> >> > >> >> > >> >> > >> >> -- > >> >> Kiely M. Donnelly, M.A. > >> >> Doctoral Candidate, Clinical Neuropsychology > >> >> University of Cincinnati > >> >> > >> >>___ > >> > Freesurfer mailing list > >> > Freesurfer@nmr.mgh.harvard.edu > >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > > > > > > -- > > Kiely M. Donnelly, M.A. > > Doctoral Candidate, Clinical Neuropsychology > > University of Cincinnati > > > > -- Kiely M. Donnelly, M.A. Doctoral Candidate, Clinical Neuropsychology University of Cincinnati ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.m
Re: [Freesurfer] trac-all -path error
The .mat registration matrix should be saved under dmri/xfms/. On Wed, 16 May 2012, Kiely Donnelly wrote: I tried using corratio and it seems to have fixed the registration issue. I'm very new to this so just want to make sure I did it correctly before I move forward. Should the command line look something like this if I am running it in this individuals dmri directory: flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz -out lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat -cost corratio Thanks so much for your help. Kiely On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan wrote: you have to run flirt commandline separately to check if it solves your problem. > Is this something I can change in my dmrirc file or do I need to run flirt > on it's own? > > Thanks, > > Kiely > > On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan < > rspr...@nmr.mgh.harvard.edu> wrote: > >> Kiely, For flirt, try using corratio, cost function instead of >> mutualinfo >> (which is the default in trac-all) to see if that solves your >> registration >> problem. >> >> >> > Hi Kiely - Looks like you used flirt for the intra-subject >> registration, >> > so you can look in trac-all.log for the flirt command line that >> registers >> > diffusion to anatomical and play around with the parameters. >> > >> > You can also use bbregister instead of flirt for the intra-subject >> > registration - it has the option to initialize with flirt or with SPM. >> > >> > Hope this helps, >> > a.y >> > >> > On Wed, 16 May 2012, Kiely Donnelly wrote: >> > >> >> Hi Priti - Thanks for your help. The inter-subject registration seems >> to >> >> have run OK, but there must be something wrong with the intra-subject >> >> registration. When I try to view it using freeview, it's completely >> dark >> >> - I >> >> don't see a brain at all. Is there a way to troubleshoot this? >> >> Thanks, >> >> >> >> Kiely >> >> >> >> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan >> >> wrote: >> >> Hi Kiely, >> >> >> >> Have you checked your inter and intra subject registrations? >> The >> >> control >> >> points going off the dwi is not only for one paths but for all >> >> the paths. >> >> If the registration goes terribly wrong, this can happen. You >> >> can take a >> >> look at >> >> >> >> /dmri/lowb_brain_anat.flt.nii.gz (For intra subject >> registration >> >> diff-anat) >> >> >> >> and >> >> >> >> /dmri/brain_anat_mni.nii.gz (For inter-subject registration >> >> anat-mni) >> >> >> >> I would start by checking that first. >> >> >> >> Priti >> >> >> >> > Hello-- >> >> > >> >> > I have run Tracula successfully for ~75 healthy subjects. >> >> However, the >> >> > pathway reconstruction seems to fail for a handful of people. >> >> I've >> >> > attached >> >> > the log file for one of these subjects. It appears that the >> >> control points >> >> > are not within the dwi. A similar problem occurred in a >> >> subject with >> >> > substantial signal loss in the dwi, but that doesn't seem to >> >> be the case >> >> > for this particular person. I have been creating the entire >> >> set of tracts, >> >> > but at this point, I'm only interested in the SLFt and SLFp. >> >> > >> >> > Thanks, >> >> > >> >> > Kiely >> >> > ___ >> >> > 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] trac-all -path error
That seemed to fix the registration issue, but I'm still unable to reconstruct the tracts using trac-all -path. I'm getting the same error that the control points are not within the mask. THis happens for all tracts. Thanks, Kiely On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > The .mat registration matrix should be saved under dmri/xfms/. > > > > On Wed, 16 May 2012, Kiely Donnelly wrote: > > I tried using corratio and it seems to have fixed the registration issue. >> I'm very new to this so just want to make sure I did it correctly before I >> move forward. Should the command line look something like this if I am >> running it in this individuals dmri directory: >> >> flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz -out >> lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat -cost corratio >> >> >> Thanks so much for your help. >> >> Kiely >> >> On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan >> wrote: >> you have to run flirt commandline separately to check if it >> solves your >> problem. >> >> >> > Is this something I can change in my dmrirc file or do I need >> to run flirt >> > on it's own? >> > >> > Thanks, >> > >> > Kiely >> > >> > On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan < >> > rspr...@nmr.mgh.harvard.edu> wrote: >> > >> >> Kiely, For flirt, try using corratio, cost function instead >> of >> >> mutualinfo >> >> (which is the default in trac-all) to see if that solves your >> >> registration >> >> problem. >> >> >> >> >> >> > Hi Kiely - Looks like you used flirt for the intra-subject >> >> registration, >> >> > so you can look in trac-all.log for the flirt command line >> that >> >> registers >> >> > diffusion to anatomical and play around with the >> parameters. >> >> > >> >> > You can also use bbregister instead of flirt for the >> intra-subject >> >> > registration - it has the option to initialize with flirt >> or with SPM. >> >> > >> >> > Hope this helps, >> >> > a.y >> >> > >> >> > On Wed, 16 May 2012, Kiely Donnelly wrote: >> >> > >> >> >> Hi Priti - Thanks for your help. The inter-subject >> registration seems >> >> to >> >> >> have run OK, but there must be something wrong with the >> intra-subject >> >> >> registration. When I try to view it using freeview, it's >> completely >> >> dark >> >> >> - I >> >> >> don't see a brain at all. Is there a way to troubleshoot >> this? >> >> >> Thanks, >> >> >> >> >> >> Kiely >> >> >> >> >> >> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan >> >> >> wrote: >> >> >> Hi Kiely, >> >> >> >> >> >> Have you checked your inter and intra subject >> registrations? >> >> The >> >> >> control >> >> >> points going off the dwi is not only for one paths >> but for all >> >> >> the paths. >> >> >> If the registration goes terribly wrong, this can >> happen. You >> >> >> can take a >> >> >> look at >> >> >> >> >> >> /dmri/lowb_brain_anat.flt.nii.**gz (For intra subject >> >> registration >> >> >> diff-anat) >> >> >> >> >> >> and >> >> >> >> >> >> /dmri/brain_anat_mni.nii.gz (For inter-subject >> registration >> >> >> anat-mni) >> >> >> >> >> >> I would start by checking that first. >> >> >> >> >> >> Priti >> >> >> >> >> >> > Hello-- >> >> >> > >> >> >> > I have run Tracula successfully for ~75 healthy >> subjects. >> >> >> However, the >> >> >> > pathway reconstruction seems to fail for a handful >> of people. >> >> >> I've >> >> >> > attached >> >> >> > the log file for one of these subjects. It appears >> that the >> >> >> control points >> >> >> > are not within the dwi. A similar problem occurred >> in a >> >> >> subject with >> >> >> > substantial signal loss in the dwi, but that >> doesn't seem to >> >> >> be the case >> >> >> > for this particular person. I have been creating >> the entire >> >> >> set of tracts, >> >> >> > but at this point, I'm only interested in the SLFt >> and SLFp. >> >> >> > >> >> >> > Thanks, >> >> >> > >> >> >> > Kiely >> >> >> > __**_ >> >> >> > Freesurfer mailing list >> >> >> > Freesurfer@nmr.mgh.harvard.edu >> >> >> > >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer
Re: [Freesurfer] trac-all -path error
Were the old .mat files replaced with the new ones? On Fri, 18 May 2012, Kiely Madhavan wrote: That seemed to fix the registration issue, but I'm still unable to reconstruct the tracts using trac-all -path. I'm getting the same error that the control points are not within the mask. THis happens for all tracts. Thanks, Kiely On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki wrote: The .mat registration matrix should be saved under dmri/xfms/. On Wed, 16 May 2012, Kiely Donnelly wrote: I tried using corratio and it seems to have fixed the registration issue. I'm very new to this so just want to make sure I did it correctly before I move forward. Should the command line look something like this if I am running it in this individuals dmri directory: flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz -out lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat -cost corratio Thanks so much for your help. Kiely On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan wrote: you have to run flirt commandline separately to check if it solves your problem. > Is this something I can change in my dmrirc file or do I need to run flirt > on it's own? > > Thanks, > > Kiely > > On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan < > rspr...@nmr.mgh.harvard.edu> wrote: > >> Kiely, For flirt, try using corratio, cost function instead of >> mutualinfo >> (which is the default in trac-all) to see if that solves your >> registration >> problem. >> >> >> > Hi Kiely - Looks like you used flirt for the intra-subject >> registration, >> > so you can look in trac-all.log for the flirt command line that >> registers >> > diffusion to anatomical and play around with the parameters. >> > >> > You can also use bbregister instead of flirt for the intra-subject >> > registration - it has the option to initialize with flirt or with SPM. >> > >> > Hope this helps, >> > a.y >> > >> > On Wed, 16 May 2012, Kiely Donnelly wrote: >> > >> >> Hi Priti - Thanks for your help. The inter-subject registration seems >> to >> >> have run OK, but there must be something wrong with the intra-subject >> >> registration. When I try to view it using freeview, it's completely >> dark >> >> - I >> >> don't see a brain at all. Is there a way to troubleshoot this? >> >> Thanks, >> >> >> >> Kiely >> >> >> >> On Wed, May 9, 2012 at 2:08 PM, Priti Srinivasan >> >> wrote: >> >> Hi Kiely, >> >> >> >> Have you checked your inter and intra subject registrations? >> The >> >> control >> >> points going off the dwi is not only for one paths but for all >> >> the paths. >> >> If the registration goes terribly wrong, this can happen. You >> >> can take a >> >> look at >> >> >> >> /dmri/lowb_brain_anat.flt.nii.gz (For intra subject >> registration >> >> diff-anat) >> >> >> >> and >> >> >> >> /dmri/brain_anat_mni.nii.gz (For inter-subject registration >> >> anat-mni) >> >> >> >> I would start by checking that first. >> >> >> >> Priti >> >> >> >> > Hello-- >> >> >
Re: [Freesurfer] trac-all -path error
I only created a diff2anat.flt.mat file which replaced the old one. Do they all need to be recreated? If so, is that something I add to the command line? On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Were the old .mat files replaced with the new ones? > > > On Fri, 18 May 2012, Kiely Madhavan wrote: > > That seemed to fix the registration issue, but I'm still unable to >> reconstruct the tracts using trac-all -path. I'm getting the same error >> that >> the control points are not within the mask. THis happens for all tracts. >> Thanks, >> >> Kiely >> >> On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki >> wrote: >> >> The .mat registration matrix should be saved under dmri/xfms/. >> >> >> On Wed, 16 May 2012, Kiely Donnelly wrote: >> >>I tried using corratio and it seems to have fixed >>the registration issue. >>I'm very new to this so just want to make sure I did >>it correctly before I >>move forward. Should the command line look something >>like this if I am >>running it in this individuals dmri directory: >> >>flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz >>-out >>lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat >>-cost corratio >> >> >>Thanks so much for your help. >> >>Kiely >> >>On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan >> wrote: >> you have to run flirt commandline separately to >>check if it >> solves your >> problem. >> >> >> > Is this something I can change in my dmrirc >>file or do I need >> to run flirt >> > on it's own? >> > >> > Thanks, >> > >> > Kiely >> > >> > On Wed, May 16, 2012 at 9:27 AM, Priti >>Srinivasan < >> > rspr...@nmr.mgh.harvard.edu> wrote: >> > >> >> Kiely, For flirt, try using corratio, cost >>function instead >> of >> >> mutualinfo >> >> (which is the default in trac-all) to see if >>that solves your >> >> registration >> >> problem. >> >> >> >> >> >> > Hi Kiely - Looks like you used flirt for >>the intra-subject >> >> registration, >> >> > so you can look in trac-all.log for the >>flirt command line >> that >> >> registers >> >> > diffusion to anatomical and play around >>with the >> parameters. >> >> > >> >> > You can also use bbregister instead of >>flirt for the >> intra-subject >> >> > registration - it has the option to >>initialize with flirt >> or with SPM. >> >> > >> >> > Hope this helps, >> >> > a.y >> >> > >> >> > On Wed, 16 May 2012, Kiely Donnelly wrote: >> >> > >> >> >> Hi Priti - Thanks for your help. The >>inter-subject >> registration seems >> >> to >> >> >> have run OK, but there must be something >>wrong with the >> intra-subject >> >> >> registration. When I try to view it using >>freeview, it's >> completely >> >> dark >> >> >> - I >> >> >> don't see a brain at all. Is there a way >>to troubleshoot >> this? >> >> >> Thanks, >> >> >> >> >> >> Kiely >> >> >> >> >> >> On Wed, May 9, 2012 at 2:08 PM, Priti >>Srinivasan >> >> >> wrote: >> >> >> Hi Kiely, >> >> >> >> >> >> Have you checked your inter and >>intra subject >> registrations? >> >> The >> >> >> control >> >> >> points going off the dwi is not >>only for one paths >> but for all >> >> >> the paths. >> >> >> If the registration goes terribly >>wrong, this can >> happen. You >> >> >> can take a >> >> >> look at >> >> >> >> >> >> /dmri/lowb_brain_anat.flt.nii.**gz >>(For intra subject >> >> registration >> >>
Re: [Freesurfer] trac-all -path error
The other registration files depend on diff2anat. For example, diff2mni is composed of diff2anat and anat2mni. If you're using the old diff2mni, it's like you didn't change anything. The -intra step creates all these. You need to edit the command that generates the diff2anat in your version of trac-preproc. Either comment that line out so that it runs everything but that, or change that line to the options that worked for you. On Fri, 18 May 2012, Kiely Madhavan wrote: I only created a diff2anat.flt.mat file which replaced the old one. Do they all need to be recreated? If so, is that something I add to the command line? On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki wrote: Were the old .mat files replaced with the new ones? On Fri, 18 May 2012, Kiely Madhavan wrote: That seemed to fix the registration issue, but I'm still unable to reconstruct the tracts using trac-all -path. I'm getting the same error that the control points are not within the mask. THis happens for all tracts. Thanks, Kiely On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki wrote: The .mat registration matrix should be saved under dmri/xfms/. On Wed, 16 May 2012, Kiely Donnelly wrote: I tried using corratio and it seems to have fixed the registration issue. I'm very new to this so just want to make sure I did it correctly before I move forward. Should the command line look something like this if I am running it in this individuals dmri directory: flirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz -out lowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat -cost corratio Thanks so much for your help. Kiely On Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan wrote: you have to run flirt commandline separately to check if it solves your problem. > Is this something I can change in my dmrirc file or do I need to run flirt > on it's own? > > Thanks, > > Kiely > > On Wed, May 16, 2012 at 9:27 AM, Priti Srinivasan < > rspr...@nmr.mgh.harvard.edu> wrote: > >> Kiely, For flirt, try using corratio, cost function instead of >> mutualinfo >> (which is the default in trac-all) to see if that solves your >> registration >> problem. >> >> >> > Hi Kiely - Looks like you used flirt for the intra-subject >> registration, >> > so you can look in trac-all.log for the flirt command line that >> registers >> > diffusion to anatomical and play around with the parameters. >> > >> > You can also use bbregister instead of flirt for the intra-subject >> > registration - it has the option to initialize with flirt or with SPM. >> > >> > Hope this helps, >> > a.y >> > >> > On Wed, 16 May 2012, Kiely Donnelly wrote: >> > >> >> Hi Priti - Thanks for your help. The inter-subject registration seems >> to >> >> have run OK, but there must be something wrong with the intra-subject >> >> registration. When I try to view it using freeview, it's completely >> da
Re: [Freesurfer] trac-all -path error
OK - Can you point me in the direction of the trac-preproc file that I should edit? On Fri, May 18, 2012 at 12:18 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > The other registration files depend on diff2anat. For example, diff2mni is > composed of diff2anat and anat2mni. If you're using the old diff2mni, it's > like you didn't change anything. > > The -intra step creates all these. You need to edit the command that > generates the diff2anat in your version of trac-preproc. Either comment > that line out so that it runs everything but that, or change that line to > the options that worked for you. > > > > On Fri, 18 May 2012, Kiely Madhavan wrote: > > I only created a diff2anat.flt.mat file which replaced the old one. Do >> they all need to be recreated? If so, is that something I >> add to the command line? >> >> On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki < >> ayend...@nmr.mgh.harvard.edu> wrote: >> >> Were the old .mat files replaced with the new ones? >> >> On Fri, 18 May 2012, Kiely Madhavan wrote: >> >>That seemed to fix the registration issue, but I'm still >> unable to >>reconstruct the tracts using trac-all -path. I'm getting the >> same error that >>the control points are not within the mask. THis happens for >> all tracts. >>Thanks, >> >>Kiely >> >>On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki >> wrote: >> >>á á áThe .mat registration matrix should be saved under >> dmri/xfms/. >> >> >>á á áOn Wed, 16 May 2012, Kiely Donnelly wrote: >> >>á á á á á áI tried using corratio and it seems to have fixed >>á á á á á áthe registration issue. >>á á á á á áI'm very new to this so just want to make sure I did >>á á á á á áit correctly before I >>á á á á á ámove forward. Should the command line look something >>á á á á á álike this if I am >>á á á á á árunning it in this individuals dmri directory:á >> >>á á á á á áflirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz >>á á á á á á-out >>á á á á á álowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat >>á á á á á á-cost corratio >> >> >>á á á á á áThanks so much for your help. >> >>á á á á á áKiely >> >>á á á á á áOn Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan >>á á á á á á wrote: >>á á á á á áá á áyou have to run flirt commandline separately to >>á á á á á ácheck if it >>á á á á á áá á ásolves your >>á á á á á áá á áproblem. >> >> >>á á á á á áá á á> Is this something I can change in my dmrirc >>á á á á á áfile or do I need >>á á á á á áá á áto run flirt >>á á á á á áá á á> on it's own? >>á á á á á áá á á> >>á á á á á áá á á> Thanks, >>á á á á á áá á á> >>á á á á á áá á á> Kiely >>á á á á á áá á á> >>á á á á á áá á á> On Wed, May 16, 2012 at 9:27 AM, Priti >>á á á á á áSrinivasan < >>á á á á á áá á á> rspr...@nmr.mgh.harvard.edu> wrote: >>á á á á á áá á á> >>á á á á á áá á á>> Kiely, For flirt, try using corratio, cost >>á á á á á áfunction instead >>á á á á á áá á áof >>á á á á á áá á á>> mutualinfo >>á á á á á áá á á>> (which is the default in trac-all) to see if >>á á á á á áthat solves your >>á á á á á áá á á>> registration >>á á á á á áá á á>> problem. >>á á á á á áá á á>> >>á á á á á áá á á>> >>á á á á á áá á á>> > Hi Kiely - Looks like you used flirt for >>á á á á á áthe intra-subject >>á á á á á áá á á>> registration, >>á á á á á áá á á>> > so you can look in trac-all.log for the >>á á á á á áflirt command line >>á á á á á áá á áthat >>á á á á á áá á á>> registers >>á á á á á áá á á>> > diffusion to anatomical and play around >>á á á á á áwith the >>á á á á á áá á áparameters. >>á á á á á áá á á>> > >>á á á á á áá á á>> > You can also use bbregister instead of >>á á á á á áflirt for the >>á á á á á áá á áintra-subject >>á á á á á áá á á>> > registration - it has the option to >>á á á á á áinitialize with flirt >>á á á á á áá á áor with SPM. >>á á á á á áá á á>> > >>á á á á á áá á á>> > Hope this helps, >>á á á á á áá á á>> > a.y >>á á á á á áá á á>> > >>á á á á á áá á á>> > On Wed, 16 May 2012, Kiely Donnelly wrote: >>á á á á á áá á á>> > >>á á á á á áá á á>> >> Hi Priti - Thanks for your help. The >>á á á á á ái
Re: [Freesurfer] trac-all -path error
This is a script, it's in the directory where all freesurfer scripts are. You can find it by doing "which trac-preproc". On Fri, 18 May 2012, Kiely Madhavan wrote: OK - Can you point me in the direction of the trac-preproc file that I should edit? On Fri, May 18, 2012 at 12:18 PM, Anastasia Yendiki wrote: The other registration files depend on diff2anat. For example, diff2mni is composed of diff2anat and anat2mni. If you're using the old diff2mni, it's like you didn't change anything. The -intra step creates all these. You need to edit the command that generates the diff2anat in your version of trac-preproc. Either comment that line out so that it runs everything but that, or change that line to the options that worked for you. On Fri, 18 May 2012, Kiely Madhavan wrote: I only created a diff2anat.flt.mat file which replaced the old one. Do they all need to be recreated? If so, is that something I add to the command line? On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki wrote: Were the old .mat files replaced with the new ones? On Fri, 18 May 2012, Kiely Madhavan wrote: That seemed to fix the registration issue, but I'm still unable to reconstruct the tracts using trac-all -path. I'm getting the same error that the control points are not within the mask. THis happens for all tracts. Thanks, Kiely On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki wrote: á á áThe .mat registration matrix should be saved under dmri/xfms/. á á áOn Wed, 16 May 2012, Kiely Donnelly wrote: á á á á á áI tried using corratio and it seems to have fixed á á á á á áthe registration issue. á á á á á áI'm very new to this so just want to make sure I did á á á á á áit correctly before I á á á á á ámove forward. Should the command line look something á á á á á álike this if I am á á á á á árunning it in this individuals dmri directory:á á á á á á áflirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz á á á á á á-out á á á á á álowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat á á á á á á-cost corratio á á á á á áThanks so much for your help. á á á á á áKiely á á á á á áOn Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan á á á á á á wrote: á á á á á áá á áyou have to run flirt commandline separately to á á á á á ácheck if it á á á á á áá á ásolves your á á á á á áá á áproblem. á á á á á áá á á> Is this something I can change in my dmrirc á á á á á áfile or do I need á á á á á áá á áto run flirt á á á á á áá á á> on it's own? á á á á á áá á á> á á á á á áá á á> Thanks, á á á á á áá á á> á á á á á áá á á> Kiely á á á á á áá á á> á á á á á áá á á> On Wed, May 16, 2012 at 9:27 AM, Priti á á á á á áSrinivasan < á á á á á áá á á> rspr...@nmr.mgh.harvard.edu> wrote: á á á á á áá á á> á á á á á áá á á>> Kiely, For flirt, try using corratio, cost á á á á á áfunction instead á á á á á áá á áof á á á á á áá á á>> mutualinfo á á á á á áá á á>> (which is the default in trac-all) to see if á á á á á áthat solves your á á á á á áá á á>> registration á á á á á áá á á>> problem. á á á á á áá á á>> á á á á á áá á á>> á á á á á áá á á>> > Hi Kiely - Looks like you used flirt for á á á á á áthe intra-subject á á á á á áá á á>> registration, á á á á á áá á á>> > so you can look in trac-all.log for the á á á á á áflirt command line á á á á á áá á áthat á á á á á áá á á>> registers á á á á á áá á á>> > diffusion to anatomical and play around á á á á á áwith the á á á á á áá á áparameters. á á á á á áá á á>> > á á á á á áá á á>> > You can also use bbregister instead of á á á á á áflirt for the á á á á á áá á áintra-subject á á á á á áá á á>> > registration - it has the option to á á á á á áinitialize with flirt á á á á á áá á áor with SPM. á á á á á áá á á>> > á á á á á áá á á>> > Hope this helps, á á á á á áá á á>> > a.y á á á á á áá á á>> > á á á á á áá á á>> > On Wed, 16 May 2012, Kiely Donnelly wrote: á á á á á áá á á>> > á á á á á áá á á>> >> Hi Priti - Thanks for your help. The á á á á á áinter-subject á á á á á áá á áregistration seems á á á á á áá á
Re: [Freesurfer] trac-all -path error
That's where I looked, but all I see is the following (I don't see the command line that creates the diff2anat for me to edit): Last login: Fri May 18 13:45:47 on ttys000 /Applications/freesurfer/bin/trac-preproc ; exit; Kielys-MacBook-Air:~ kielydonnelly$ /Applications/freesurfer/bin/trac-preproc ; exit; USAGE: trac-preproc Required arguments: -c : dmrirc file (see dmrirc.example) Other arguments: -log : default is trac-all.log in the same dir as dmrirc -nolog : do not save a log file -cmd : default is trac-all.cmd in the same dir as dmrirc -nocmd : do not save a cmd file -no-isrunning : do not check whether this subject is currently being processed -umask umask : set unix file permission mask (default 002) -grp groupid : check that current group is alpha groupid -allowcoredump : set coredump limit to unlimited -debug : generate much more output -dontrun : do everything but execute each command -version : print version of this script and exit -help : print full contents of help logout [Process completed] On Fri, May 18, 2012 at 1:59 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > This is a script, it's in the directory where all freesurfer scripts are. > You can find it by doing "which trac-preproc". > > > On Fri, 18 May 2012, Kiely Madhavan wrote: > > OK - Can you point me in the direction of the trac-preproc file that I >> should edit? >> >> On Fri, May 18, 2012 at 12:18 PM, Anastasia Yendiki < >> ayend...@nmr.mgh.harvard.edu> wrote: >> >> The other registration files depend on diff2anat. For example, >> diff2mni is composed of diff2anat and anat2mni. If >> you're using the old diff2mni, it's like you didn't change anything. >> >> The -intra step creates all these. You need to edit the command that >> generates the diff2anat in your version of >> trac-preproc. Either comment that line out so that it runs >> everything but that, or change that line to the options >> that worked for you. >> >> >> On Fri, 18 May 2012, Kiely Madhavan wrote: >> >> I only created a diff2anat.flt.mat file which replaced the old one. >> Do they all need to be recreated? If so, >> is that something I >> add to the command line? >> >> On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki < >> ayend...@nmr.mgh.harvard.edu> wrote: >> >> Were the old .mat files replaced with the new ones? >> >> On Fri, 18 May 2012, Kiely Madhavan wrote: >> >> That seemed to fix the registration issue, but I'm still >> unable to >> reconstruct the tracts using trac-all -path. I'm getting >> the same error that >> the control points are not within the mask. THis happens >> for all tracts. >> Thanks, >> >> Kiely >> >> On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki >> wrote: >> >>á á áThe .mat registration matrix should be saved under >> dmri/xfms/. >> >> >>á á áOn Wed, 16 May 2012, Kiely Donnelly wrote: >> >>á á á á á áI tried using corratio and it seems to have fixed >>á á á á á áthe registration issue. >>á á á á á áI'm very new to this so just want to make sure I did >>á á á á á áit correctly before I >>á á á á á ámove forward. Should the command line look something >>á á á á á álike this if I am >>á á á á á árunning it in this individuals dmri directory:á >> >>á á á á á áflirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz >>á á á á á á-out >>á á á á á álowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat >>á á á á á á-cost corratio >> >> >>á á á á á áThanks so much for your help. >> >>á á á á á áKiely >> >>á á á á á áOn Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan >>á á á á á á wrote: >>á á á á á áá á áyou have to run flirt commandline separately to >>á á á á á ácheck if it >>á á á á á áá á ásolves your >>á á á á á áá á áproblem. >> >> >>á á á á á áá á á> Is this something I can change in my dmrirc >>á á á á á áfile or do I need >>á á á á á áá á áto run flirt >>á á á á á áá á á> on it's own? >>á á á á á áá á á> >>á á á á á áá á á> Thanks, >>á á á á á áá á á> >>á á á á á áá á á> Kiely >>á á á á á áá á á> >>á á á á á áá á á> On Wed, May 16, 2012 at 9:27 AM, Priti >>á á á á á áSrinivasan < >>á á á á á áá á á> rspr...@nmr.mgh.harvard.edu> wrote: >>á á á á á áá á á> >>á á á á á áá á á>> Kiely, For flirt, try using corratio, cost >>á á á á á áfunction instead >>á á á á á áá á áof >>á á á á á áá á á>> mutualinfo >
Re: [Freesurfer] trac-all -path error
This is the help text that you get when you run the script. You need to open the script in a text editor. On Fri, 18 May 2012, Kiely Madhavan wrote: That's where I looked, but all I see is the following (I don't see the command line that creates the diff2anat for me to edit): Last login: Fri May 18 13:45:47 on ttys000 /Applications/freesurfer/bin/trac-preproc ; exit; Kielys-MacBook-Air:~ kielydonnelly$ /Applications/freesurfer/bin/trac-preproc ; exit; USAGE: trac-preproc Required arguments: -c : dmrirc file (see dmrirc.example) Other arguments: -log : default is trac-all.log in the same dir as dmrirc -nolog : do not save a log file -cmd : default is trac-all.cmd in the same dir as dmrirc -nocmd : do not save a cmd file -no-isrunning : do not check whether this subject is currently being processed -umask umask : set unix file permission mask (default 002) -grp groupid : check that current group is alpha groupid -allowcoredump : set coredump limit to unlimited -debug : generate much more output -dontrun : do everything but execute each command -version : print version of this script and exit -help : print full contents of help logout [Process completed] On Fri, May 18, 2012 at 1:59 PM, Anastasia Yendiki wrote: This is a script, it's in the directory where all freesurfer scripts are. You can find it by doing "which trac-preproc". On Fri, 18 May 2012, Kiely Madhavan wrote: OK - Can you point me in the direction of the trac-preproc file that I should edit? On Fri, May 18, 2012 at 12:18 PM, Anastasia Yendiki wrote: The other registration files depend on diff2anat. For example, diff2mni is composed of diff2anat and anat2mni. If you're using the old diff2mni, it's like you didn't change anything. The -intra step creates all these. You need to edit the command that generates the diff2anat in your version of trac-preproc. Either comment that line out so that it runs everything but that, or change that line to the options that worked for you. On Fri, 18 May 2012, Kiely Madhavan wrote: I only created a diff2anat.flt.mat file which replaced the old one. Do they all need to be recreated? If so, is that something I add to the command line? On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki wrote: Were the old .mat files replaced with the new ones? On Fri, 18 May 2012, Kiely Madhavan wrote: That seemed to fix the registration issue, but I'm still unable to reconstruct the tracts using trac-all -path. I'm getting the same error that the control points are not within the mask. THis happens for all tracts. Thanks, Kiely On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki wrote: á á áThe .mat registration matrix should be saved under dmri/xfms/. á á áOn Wed, 16 May 2012, Kiely Donnelly wrote: á á á á á áI tried using corratio and it seems to have fixed á á á á á áthe registration issue. á á á á á áI'm very new to this so just want to make sure I did á á á á á áit correctly before I á á á á á ámove forward. Should the command line look something á á á á á álike this if I am á á á á á árunning it in this individuals dmri directory:á á á á á á áflirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz á á á á á á-out á á á á á álowb_brain_anat.flt.nii.gz -omat diff2anat.flt.mat á á á á á á-cost corratio á á á á á áThanks so much for your help. á á á á á áKiely á á á á á áOn Wed, May 16, 2012 at 10:12 AM, Priti Srinivasan á á á á á á wrote: á á á á á áá á áyou have to run flirt commandline separately to á á á á á ácheck if it á á á á á áá á ásolves your á á á á á áá á áproblem. á á á á á áá á á> Is this something I can change in my dmrirc á á á á á áfile or do I need á á á á á áá á áto run flirt á á á á á áá á á> on it's own? á á á á á áá á á> á á á á á áá á á> Thanks,
Re: [Freesurfer] trac-all -path error
Hi Kiely, In your terminal (after sourcing the freesurfer environment) type the following: gedit $FREESURFER_HOME/bin/trac-preproc (use pico if you're using mac, you can also use other editors like vi or emacs) This will open up trac-preproc script in a text editor. you can scroll through to #--- Intra-subject registration # in the script and look for the following lines: if ($doregflt) then # Register low-b to anatomical using flirt set cmd = flirt set cmd = ($cmd -in $dwidir/lowb_brain.nii.gz) set cmd = ($cmd -ref $dwidir/brain_anat.nii.gz) set cmd = ($cmd -out $dwidir/lowb_brain_anat.flt.nii.gz) set cmd = ($cmd -omat $xfmdir/diff2anat.flt.mat) set cmd = ($cmd -cost mutualinfo) echo $cmd |& tee -a $LF |& tee -a $CF if ($RunIt) then $fs_time $cmd |& tee -a $LF if ($status) goto error_exit endif Change the mutualinfo in the above line to corratio Re-run trac-all -intra -inter -masks -tensor -prior -c and then trac-all -path Best, Priti > That's where I looked, but all I see is the following (I don't see the > command line that creates the diff2anat for me to edit): > > > Last login: Fri May 18 13:45:47 on ttys000 > /Applications/freesurfer/bin/trac-preproc ; exit; > Kielys-MacBook-Air:~ kielydonnelly$ > /Applications/freesurfer/bin/trac-preproc ; exit; > > USAGE: trac-preproc > > Required arguments: > -c : dmrirc file (see dmrirc.example) > > Other arguments: > -log : default is trac-all.log in the same dir as dmrirc > -nolog : do not save a log file > -cmd : default is trac-all.cmd in the same dir as dmrirc > -nocmd : do not save a cmd file > -no-isrunning : do not check whether this subject is currently being > processed > -umask umask : set unix file permission mask (default 002) > -grp groupid : check that current group is alpha groupid > -allowcoredump : set coredump limit to unlimited > -debug : generate much more output > -dontrun : do everything but execute each command > -version : print version of this script and exit > -help : print full contents of help > > logout > > [Process completed] > > On Fri, May 18, 2012 at 1:59 PM, Anastasia Yendiki < > ayend...@nmr.mgh.harvard.edu> wrote: > >> >> This is a script, it's in the directory where all freesurfer scripts >> are. >> You can find it by doing "which trac-preproc". >> >> >> On Fri, 18 May 2012, Kiely Madhavan wrote: >> >> OK - Can you point me in the direction of the trac-preproc file that I >>> should edit? >>> >>> On Fri, May 18, 2012 at 12:18 PM, Anastasia Yendiki < >>> ayend...@nmr.mgh.harvard.edu> wrote: >>> >>> The other registration files depend on diff2anat. For example, >>> diff2mni is composed of diff2anat and anat2mni. If >>> you're using the old diff2mni, it's like you didn't change >>> anything. >>> >>> The -intra step creates all these. You need to edit the command >>> that >>> generates the diff2anat in your version of >>> trac-preproc. Either comment that line out so that it runs >>> everything but that, or change that line to the options >>> that worked for you. >>> >>> >>> On Fri, 18 May 2012, Kiely Madhavan wrote: >>> >>> I only created a diff2anat.flt.mat file which replaced the old >>> one. >>> Do they all need to be recreated? If so, >>> is that something I >>> add to the command line? >>> >>> On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki < >>> ayend...@nmr.mgh.harvard.edu> wrote: >>> >>> Were the old .mat files replaced with the new ones? >>> >>> On Fri, 18 May 2012, Kiely Madhavan wrote: >>> >>> That seemed to fix the registration issue, but I'm >>> still >>> unable to >>> reconstruct the tracts using trac-all -path. I'm >>> getting >>> the same error that >>> the control points are not within the mask. THis >>> happens >>> for all tracts. >>> Thanks, >>> >>> Kiely >>> >>> On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki >>> wrote: >>> >>>á á áThe .mat registration matrix should be saved under >>> dmri/xfms/. >>> >>> >>>á á áOn Wed, 16 May 2012, Kiely Donnelly wrote: >>> >>>á á á á á áI tried using corratio and it seems to have fixed >>>á á á á á áthe registration issue. >>>á á á á á áI'm very new to this so just want to make sure I >>> did >>>á á á á á áit correctly before I >>>á á á á á ámove forward. Should the command line look >>> something >>>á á á á á álike this if I am >>>á á á á á árunning it in this individuals dmri directory:á >>> >>>á á á á á áflirt -in dwi_orig.nii.gz -ref brain_anat.nii.gz >>>á á á á á á-out >>>á á á á á álowb_brain_anat.flt.nii.gz -omat >>> diff2anat.flt.mat >>>á á á á á á-cost corratio >
Re: [Freesurfer] trac-all -path error
Wonderful - thank you. That seemed to fix the problem. Kiely On Fri, May 18, 2012 at 3:25 PM, Priti Srinivasan < rspr...@nmr.mgh.harvard.edu> wrote: > Hi Kiely, > > In your terminal (after sourcing the freesurfer environment) type the > following: > > gedit $FREESURFER_HOME/bin/trac-preproc (use pico if you're using mac, you > can also use other editors like vi or emacs) > > This will open up trac-preproc script in a text editor. > > you can scroll through to #--- Intra-subject registration # > > in the script and look for the following lines: > > > if ($doregflt) then ># Register low-b to anatomical using flirt >set cmd = flirt >set cmd = ($cmd -in $dwidir/lowb_brain.nii.gz) >set cmd = ($cmd -ref $dwidir/brain_anat.nii.gz) >set cmd = ($cmd -out $dwidir/lowb_brain_anat.flt.nii.gz) >set cmd = ($cmd -omat $xfmdir/diff2anat.flt.mat) >set cmd = ($cmd -cost mutualinfo) >echo $cmd |& tee -a $LF |& tee -a $CF >if ($RunIt) then > $fs_time $cmd |& tee -a $LF > if ($status) goto error_exit >endif > > Change the mutualinfo in the above line to corratio > > Re-run trac-all -intra -inter -masks -tensor -prior -c > and then trac-all -path > > Best, > Priti > > > > > > That's where I looked, but all I see is the following (I don't see the > > command line that creates the diff2anat for me to edit): > > > > > > Last login: Fri May 18 13:45:47 on ttys000 > > /Applications/freesurfer/bin/trac-preproc ; exit; > > Kielys-MacBook-Air:~ kielydonnelly$ > > /Applications/freesurfer/bin/trac-preproc ; exit; > > > > USAGE: trac-preproc > > > > Required arguments: > > -c : dmrirc file (see dmrirc.example) > > > > Other arguments: > > -log : default is trac-all.log in the same dir as dmrirc > > -nolog : do not save a log file > > -cmd : default is trac-all.cmd in the same dir as dmrirc > > -nocmd : do not save a cmd file > > -no-isrunning : do not check whether this subject is currently being > > processed > > -umask umask : set unix file permission mask (default 002) > > -grp groupid : check that current group is alpha groupid > > -allowcoredump : set coredump limit to unlimited > > -debug : generate much more output > > -dontrun : do everything but execute each command > > -version : print version of this script and exit > > -help : print full contents of help > > > > logout > > > > [Process completed] > > > > On Fri, May 18, 2012 at 1:59 PM, Anastasia Yendiki < > > ayend...@nmr.mgh.harvard.edu> wrote: > > > >> > >> This is a script, it's in the directory where all freesurfer scripts > >> are. > >> You can find it by doing "which trac-preproc". > >> > >> > >> On Fri, 18 May 2012, Kiely Madhavan wrote: > >> > >> OK - Can you point me in the direction of the trac-preproc file that I > >>> should edit? > >>> > >>> On Fri, May 18, 2012 at 12:18 PM, Anastasia Yendiki < > >>> ayend...@nmr.mgh.harvard.edu> wrote: > >>> > >>> The other registration files depend on diff2anat. For example, > >>> diff2mni is composed of diff2anat and anat2mni. If > >>> you're using the old diff2mni, it's like you didn't change > >>> anything. > >>> > >>> The -intra step creates all these. You need to edit the command > >>> that > >>> generates the diff2anat in your version of > >>> trac-preproc. Either comment that line out so that it runs > >>> everything but that, or change that line to the options > >>> that worked for you. > >>> > >>> > >>> On Fri, 18 May 2012, Kiely Madhavan wrote: > >>> > >>> I only created a diff2anat.flt.mat file which replaced the old > >>> one. > >>> Do they all need to be recreated? If so, > >>> is that something I > >>> add to the command line? > >>> > >>> On Fri, May 18, 2012 at 10:55 AM, Anastasia Yendiki < > >>> ayend...@nmr.mgh.harvard.edu> wrote: > >>> > >>> Were the old .mat files replaced with the new ones? > >>> > >>> On Fri, 18 May 2012, Kiely Madhavan wrote: > >>> > >>> That seemed to fix the registration issue, but I'm > >>> still > >>> unable to > >>> reconstruct the tracts using trac-all -path. I'm > >>> getting > >>> the same error that > >>> the control points are not within the mask. THis > >>> happens > >>> for all tracts. > >>> Thanks, > >>> > >>> Kiely > >>> > >>> On Wed, May 16, 2012 at 11:39 AM, Anastasia Yendiki > >>> wrote: > >>> > >>>á á áThe .mat registration matrix should be saved under > >>> dmri/xfms/. > >>> > >>> > >>>á á áOn Wed, 16 May 2012, Kiely Donnelly wrote: > >>> > >>>á á á á á áI tried using corratio and it seems to have fixed > >>>á á á á á áthe registration issue. > >>>á á á á á áI'm very new to this so just want to make sure I > >>> did > >>>á á á á á áit correctly before I > >>>á
Re: [Freesurfer] trac-all -path error "Segmentation Fault (Core Dumped)"
Hi Thomas - No bother at all! If you search for the word "error" in your trac-all.log, you'll see that it couldn't find the MNI template, which means that some of the pre-processing steps did not complete. You can either remove the "mnitemp" line from your configuration file (so that it uses the default $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz) or edit that line to include the correct path to the MNI template. You'll then need to rerun the pre-processing, or at least the steps including the inter-subject registration and beyond (run trac-all without arguments to see the sequence of steps included in the pre-processing). Hope this helps, a.y On Wed, 10 Dec 2014, Thomas DeRamus wrote: > Freesurfer Experts, > > Sorry to bother you again, but I'm having an issue with the 3rd step of > Tracula. I was able to run -prep just fine, and I ran bedpostx locally > (there was an error in the step 2 command apparently, used command "bedpostx > ///dmri/"), but every time I run the third step with the -path > command I get the error "Segmentation fault (core dumped) foreach: No > match." > > The foreach error has me thinking there is something wrong with my dmrirc > file or my folder structure. > > I'd appreciate any feedback you are willing to give on this error. > > I've attached the trac-all.log for one subject, but it gives the same error > even when different subjects are used or this one is removed. > > -- > Thomas DeRamusUAB Department of Psychology, Behavioral Neuroscience > Graduate Research Trainee > Civitan International Research Center > 1719 6th Ave S, Suite 235J, Birmingham, AL 35233 > Phone: 205-934-0971 Email: tpdera...@gmail.com, faus...@uab.edu > > ___ 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] trac-all -path error "Segmentation Fault (Core Dumped)"
Ack. Can't believe I missed that. Thank you. I'll run it again and see how that turns out. On Thu, Dec 11, 2014 at 2:07 PM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Thomas - No bother at all! If you search for the word "error" in your > trac-all.log, you'll see that it couldn't find the MNI template, which > means that some of the pre-processing steps did not complete. You can > either remove the "mnitemp" line from your configuration file (so that it > uses the default $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz) or edit > that line to include the correct path to the MNI template. You'll then > need to rerun the pre-processing, or at least the steps including the > inter-subject registration and beyond (run trac-all without arguments to > see the sequence of steps included in the pre-processing). > > Hope this helps, > a.y > > On Wed, 10 Dec 2014, Thomas DeRamus wrote: > > > Freesurfer Experts, > > > > Sorry to bother you again, but I'm having an issue with the 3rd step of > > Tracula. I was able to run -prep just fine, and I ran bedpostx locally > > (there was an error in the step 2 command apparently, used command > "bedpostx > > ///dmri/"), but every time I run the third step with the > -path > > command I get the error "Segmentation fault (core dumped) foreach: No > > match." > > > > The foreach error has me thinking there is something wrong with my dmrirc > > file or my folder structure. > > > > I'd appreciate any feedback you are willing to give on this error. > > > > I've attached the trac-all.log for one subject, but it gives the same > error > > even when different subjects are used or this one is removed. > > > > -- > > Thomas DeRamusUAB Department of Psychology, Behavioral Neuroscience > > Graduate Research Trainee > > Civitan International Research Center > > 1719 6th Ave S, Suite 235J, Birmingham, AL 35233 > > Phone: 205-934-0971 Email: tpdera...@gmail.com, faus...@uab.edu > > > > > ___ > 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. > > -- *Thomas DeRamus* UAB Department of Psychology, Behavioral Neuroscience Graduate Research Trainee Civitan International Research Center 1719 6th Ave S, Suite 235J, Birmingham, AL 35233 *Phone*: 205-934-0971 *Email:* tpdera...@gmail.com, faus...@uab.edu ___ 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.
