Hi Sasha,
that's probably your problem - that mris_ca_label wasn't rerun and you
are looking at a parcellation associated with an old surface that no
longer exists. Did recon-all end with an error?
Bruce
On Mon, 14 Nov 2005, Sasha Wolosin wrote:
I looked through the recon-all.log file, but I could not find any
references to mris_ca_label or mris_anatomical_stats, do you know what
else I can search for?
I found this warning in several places, but I don't know if it is
related:
INFO: Volume /tmp/mritotal_12360/orig_8_dxyz.mnc cannot be found.
In the recon-all.status file there is another warning:
Euler: NHoles =
WARNING: Number of holes is not zero
This subject was previously manually edited with an older version (oct
2003 release).
I made four copies of the subject and ran each of the following in both
the 2003 release and the latest stable release:
recon-all -subjid subject -stage3 -stage4a -stage4b
recon-all -subjid subject -all
I only saw the warnings in subjects run with the stable release, (in the
2003 release NHoles =0).
Could I be missing some files?
Thanks,
Sasha
Xiao Han <[EMAIL PROTECTED]> >>>
If you run "recon-all -all ...", then mris_ca_label and
mris_anatomical_stats should be included as the final two steps.
You can check the recon-all.log file under each subject's script
directory
to see why mris_ca_label wasn't executed in your previous run of
recon-all.
-Xiao
On Mon, 14 Nov 2005, Sasha Wolosin wrote:
That might have been what happened. I loaded the annotation to the
other surfaces, but they also looked strange. Then I re-ran
mris_ca_label and the labels look normal.
So are mris_ca_label and mris_anatomical_stats not part of the
recon-all
script (I am using the stable release)?
Thanks,
Sasha
Xiao Han <[EMAIL PROTECTED]> >>>
hmm, that's wierd.
Did you recomputed the white surface after the annotation file was
generated?
You can try to load the annotation to other surfaces of the same
hemisphere, like ?h.sphere, ?h.sphere.reg, to see whether the same
scattered appearance still exists.
-Xiao
On Mon, 14 Nov 2005, Sasha Wolosin wrote:
I double-checked, the correct hemisphere is loaded
Xiao Han <[EMAIL PROTECTED]> >>>
It's not normal.
It's very likely that you load a rh annotation to a lh surface or the
other way around. Pls double check.
-Xiao
On Mon, 14 Nov 2005, Sasha Wolosin wrote:
Dear all,
When I load the ?h.aparc.annot with the ?h.white surface in
tksurfer,
the labels look very scattered, is this normal? (please see
attached
jpeg)
Thanks,
Sasha
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