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
<ayend...@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-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf
of Anastasia Yendiki [ayend...@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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