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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