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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