The symlinks are actually created in the -bedp step, not the -prep step. If you're running bedpostx outside of trac-all, you need to create them yourself.

On Thu, 16 Aug 2012, Watson, Christopher wrote:

I've just taken to making the sym links myself after running trac-prep and before running bedpostx. Then everything should run normally. ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu] Sent: Thursday, August 16, 2012 4:24 PM To: Richard Binney Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] TRACULA -prep error

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

I'm thinking now maybe it's a good idea to move the symlink creation to the -prep part, to make it easier for anyone who ever needs to run bedpostx outside trac-all. Thanks for bringing this up.

On Thu, 16 Aug 2012, Richard Binney wrote:

Yes, because of the directions given previous listing I am running bedpost outside of trac-all (is this not necessary anymore - have we a new update?)

I do not remember having to manually create the symlinks last time around but I have just done that now and bedpost is whirring away happily.

For future reference to other TRACULA users:

dmri/data.nii.gz should be a symlink to dmri/dwi.nii.gz

presumably only if you have usemaskanat=1, then: dmri/nodif_brain_mask.nii.gz should be linked to dlabel/diff/aparc+aseg_mask.bbr.nii.gz

Otherwise I guess it would be linked to the dmri/lowb_brain.nii.gz, but someone may correct me on that and some of the above.

Thanks for your help eveyone

Richard

On Thu, Aug 16, 2012 at 2:24 PM, Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu wrote:

  The symlinks are actually created in the -bedp step, not the
  -prep step. If you're running bedpostx outside of trac-all, you
  need to create them yourself.

  On Thu, 16 Aug 2012, Watson, Christopher wrote:

        I've just taken to making the sym links myself after
        running trac-prep and before running bedpostx. Then
        everything should run normally.
        ________________________________________
        From: freesurfer-bounces@nmr.mgh.harvard.edu
        [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf
        of Anastasia Yendiki [ayendiki@nmr.mgh.harvard.edu]
        Sent: Thursday, August 16, 2012 4:24 PM
        To: Richard Binney
        Cc: freesurfer@nmr.mgh.harvard.edu
        Subject: Re: [Freesurfer] TRACULA -prep error

        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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