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

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