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
