Hi,
I recently ran into a problem with some of my tal registrations during
the recon-all process (see below message to Martino's Tech). In order
to fix the problem, it was suggested that we run bbregister outside of
the recon-all stream and then feed that registration into the
subsequent recon stages. Does this make sense, and how would I go
about doing this? I'm not sure what the --mov file should be, or if
there is a way to specify fstal as the reference structural.
Thanks for your help!
-Garth
Hi Doug & FreeSurfers,
I recently re-ran a large number of recons and have been checking to
make sure
they all ran correctly, and I have come up with a couple of questions
about the
talairach transform/recon checking.
For some of my recons, the green line outlining the white matter on the
individual brain extends slightly further than the cortex surface of
the fstal
brain. While it looks relatively well aligned (e.g. ventricles, brain
stem), the
fstal brain looks slightly too small for the subject's brain.
Additionally, the
green outline tends to extend into the skull of fstal in the sagittal
plane. An
example is:
setenv SUBJECTS_DIR /autofs/space/brownie_003/users/gcoombs/
SUBJECTS_DIR/
tkregister2 --mgz --fstal --surf orig --s amac_anat
or
tkregister2 --mgz --fstal --surf orig --s amra_anat
In order to fix these talairach transforms, it seems like the best
option would
be to scale the brain; however, we will be doing a cortical thickness
analysis
on this group, and we do not want to scale the brain if it will
somehow affect
the outcomes. Is this something we should worry about?
Another question we have is about general recon quality control: when
checking
that the recons ran smoothly, what should we look for? I look to make
sure that
the pial and white matter surface lines don't include dura or any
other matter
and that they follow the structures correctly, skull stripping, and
intensity
normalization, but is there anything else that is particularly
important?
Any advice would be greatly appreciated!
Thanks,
Garth
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