Did you check the skull strip? You can send it to us if you want and
we will take a look.
On Jun 15, 2009, at 10:43 AM, Deane Aikins <deane.aik...@yale.edu>
wrote:
Hi Bruce-
Agreed. Visual check of talairach looks good and manual correction
of slight
sagital angle fails to improve z value, hence the current notal-check.
Looking at recon-all.log, there is a statement that The surface
validation has
detected a possible Error", with a suggestion to use the '-atlas'
option if the
final seg is not valid. Also, it's saying that brainmask.mgz
already exists and
that I would need to add -clean-bm to overwrite brainmask.mgz. \n
Is any of that information of use?
Deane
Quoting Bruce Fischl <fis...@nmr.mgh.harvard.edu>:
Hi Deanne,
something is badly wrong - that step should only take a couple of
minutes.
Did you check the talairach visually? It may need to be manually
corrected.
cheers
Bruce
On Fri, 12 Jun 2009, Deane Aikins wrote:
I'm rerunning it with -no-talcheck. It looks to be hanging on
finding
control
points in the Left_Cerebral_White_matter. Can this one step take
more than
24
hrs? The "usual" time for a recon-all was @30 hrs for the other
brains.
Thanks,
Deane
Quoting Nick Schmansky <ni...@nmr.mgh.harvard.edu>:
Deane,
the -no-talcheck flag is your best option now, considering that a
manual
alignment is no better than the automatic.
What is the age range of your subjects? We're implementing an
alternate
target consisting of young adults scanned at 3T, which works
better for
that cohort over the adults in the default target we use.
Nick
On Fri, 2009-06-12 at 09:43 -0400, Deane Aikins wrote:
Hello,
I had a Talairach QA check failure, with the error log
indicating a Z =
-8
which
was below the criterion of z =-6.
I then used tkregister2 to attempt a manual alignment (no surf
orig was
available). After visual inspection, the subject and Talairach
volumes
looked
really closely aligned already. I did some very conservative
rotation
and
movement in the sagital plane, checked other planes, hit "SAVE
REG" and
then
executed
recon-all -all -subjid MYFILENAMEHERE
in the subj directory. I then get the same error, with the same
z score.
I've
tried several alignments (very little adjustment each time) with
the same
results.
I notice that when I hit SAVE REG there is a new 4 x 4 numerical
matrix
written
to my xterm screen. The values look very very similar to those
prior.
Is there a way to interpret these values to assist me in my manual
alignment?
Should I just bag it and use -notal-check? The majority of my
patient
set
ran
without errors.
Thank you!
Deane Aikins, PhD
Director, Cognitive Neuroscience Laboratory
National Center for PTSD Clinical Neuroscience Division
Assistant Professor, Department of Psychiatry
Yale School of Medicine
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