[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
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