Hello all,

I recently created a .gca atlas for a set of special subjects. After running recon-all for one of these subjects, I was left with the following error during the 'Subcortical Segmentation' section:

searching scale 1 Z rot 6.8 global minimum found at slice 0.0, rotations (90.00, -0.00)

final transformation (x=0.0, yr=90.000, zr=-0.000):

-0.000 0.000 1.000 128.000;

-0.000 1.000 -0.000 128.000;

-1.000 0.000 0.000 128.000;

0.000 0.000 0.000 1.000;

Segmentation fault

I also attached a copy of the .gca atlas, the labels.mgz file, and the LUT I am using.

Right now I have two probable causes of the problem:

1.) Since I did not include all of the regions as the normal .gca atlas, recon-all may be exiting with error. [I only included the following regions for labels: caudate, white matter, gray matter, cortex, thalamus, hippocampus, parahippocampus, putamen, pallidum, and amygdala].

2.) I used a different look-up table [LUT] with different segmentation values for the previously listed regions.

Do you think that either of these could be the reason for the segmentation fault? Any ideas on how to get around it?

Thanks in advance.

Best,

atlas.gca