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
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