Dear Freesurfers,
I haven't been able to run recon-all in a set of subjects. All them stop at the point of the talairach transform verification. I uploaded one of the files here (5.3MB): http://dl.getdropbox.com/u/74925/20070404.nii.zip
For that volume, the transform.xfm file looked indeed odd (m22=7.2??):
1.39488649 0.08332049 0.01164643 3.51684260 -0.14383204 7.20834160 -2.21084833 11.16247082 -0.16614650 1.02134335 1.85208952 -45.74753189
Using flirt (flirt -in 20070404.nii -ref MNI152_T1_1mm -out 20070404trans.nii -omat 20070404trans.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12 -interp trilinear), the transformation was:
1.05366 -0.050378 0.0606504 4.05766 0.0446432 1.09476 0.1321 -28.652 -0.058117 -0.180136 1.09158 31.7066 0 0 0 1
The voxel size of the volume is 1.17x1.17x1.2, so it shouldn't be a problem of resolution.
When I converted the volume to mgz (mri_convert 20070404.nii mri/orig/001.mgz), the orientation was wrong; but changing it using the Volume Tools in tkmedit did not alter the outcome...
Finally, I also used the --notal-check switch in recon-all, but then the script failed before completing skull stripping...
thank you very much in advance for your help!
roberto