Could you pls forward the recon-all.log file to me? mris_ca_label should be part of -stage4b.
-Xiao
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 xhan@nmr.mgh.harvard.edu >>>
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 xhan@nmr.mgh.harvard.edu >>>
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 xhan@nmr.mgh.harvard.edu >>>
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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