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
