voila....thanks for your help

On Thu, Aug 16, 2012 at 2:09 PM, Anastasia Yendiki < ayendiki@nmr.mgh.harvard.edu> wrote:

Can you send me trac-all.log?

On Thu, 16 Aug 2012, Richard Binney wrote:

So looking back at my previous successful attempts, it appears that both

...

data.nii.gz and nodif_brain_mask.nii.gz should be symbolic links (to dwi and lowb_, presumably). that correct?

So for some reason these symbolic links were not created. I wasn't over-writing. It was a fresh run on a previously non-existent directory (the trac-all script automatically creates a new subject-specific directory in my TRACULA_output directory [specified in dmrirc]).

The control.dat file is an oddity. It appears to be a control points file from the RECON output and has a modification date 2 days after the -prep was run and on the day (but a few hours before) I ran bedpost (wierdly it has a write date of 1969). I have no idea what has happened here. May have been a random copying/saving error I made at some point (???? :s)

Forgetting control.dat, what do you think could be happening here?

Many thanks for your help.

Richard

On Thu, Aug 16, 2012 at 1:24 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

  Hi Richard - In the listing you sent below I do see the a
  nodif_brain_mask.nii.gz and a control.dat, although I have no
  idea what control.dat is. As for data.nii.gz, it should be
  created as a symbolic link to dwi.nii.gz, since bedpostx indeed
  expects it to be called "data". I have not seen this problem
  before, but does it occur only when you rerun and overwrite
  things in the same directory, or also when you start a fresh run
  on a previously non-existent directory?

  a.y

  On Thu, 16 Aug 2012, Richard Binney wrote:

        Hi Anastasia et al.,

        I previously had TRACULA running wonderfully on a
        test dataset. I was tasked
        with writing an in-house step-by-step manual for
        dummies. Since then, a
        colleague has followed my manual with a new dataset
        and had problems. After
        trying to determine whether it was her install or
        something about her data
        and failing to find anything, I returned to re-run
        the subject I had already
        successfully processed. Nothing has changed in my
        install (TRAC-all version
        etc) ODDLY, this re-run is suffering from the same
        problem as my colleague.

        We ran trac-all -prep -dmrirc and it exited without
        any errors. However,
        there seem to be some files missing from the output:

        control.dat

        data.nii.gz

        nodif_brain_mask.nii.gz



        Bedpostx will not run due to the data file being
        missing and I'm sure the
        other missing files will cause problems.

        What is going on?

        I knew to look for these files as at some point I
        found the following list
        for the \dmri\. I can not re-find a post with this
        list so I'm sorry if it
        related to a solution to our current problem.

        Please help

        Richard

        brain_anat_mni.nii.gz

        dtifit_L2.nii.gz  dwi_orig_flip.nii.gz

        brain_anat.nii.gz

        dtifit_L3.nii.gz

        dwi_orig.mghdti.bvals

        brain_anat_orig.nii.gz  dtifit_MD.nii.gz

        dwi_orig.mghdti.bvecs

        bvals

        dtifit_MO.nii.gz  dwi_orig.nii.gz

        bvecs

        dtifit_S0.nii.gz  dwi_snr.txt

        bvecs.norot

        dtifit_V1.nii.gz  lowb_brain.nii.gz

        control.dat

        dtifit_V2.nii.gz

        lowb.nii.gz

        data.nii.gz

        dtifit_V3.nii.gz

        mni

        dtifit_FA.nii.gz

        dwi.ecclog

        nodif_brain_mask.nii.gz

        dtifit_L1.nii.gz

        dwi.nii.gz

         xfms

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