Yes, I use "brain images" produced by bet. But BrainParcellation does not finish. It stops sometime after writing something like

Setting subsampling
Setting reg mode
Setting lambda

several times in PartitionTemplate2FA_00001.log. But then suddenly this file disappears after the process has stopped.

After changing parameters in bet and catching some output of PartitionTemplate2FA_00001.log with "tail -f" I got the follwing messages:

# tail -f ./logs/PartitionTemplate2FA_00001.log
Setting lambda
Setting subsampling
Setting reg mode
Setting lambda
SpMat::SolveForx: Warning requested tolerence not obtained.
Requested tolerance was 0.001, and achieved tolerance was 0.0256171
This may or may not be a problem in your application, but you should look into it
Setting subsampling
Setting reg mode
Setting lambda
Setting subsampling
Setting reg mode
Setting lambda
invwarp -w /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp -r /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2.nii.gz -o /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv
 
WARNING!! Reference image has large non-zero ROI. Check that BET has run successfully on this.
 
applywarp -i /opt/spm/PANDA-1.1.0_64/data/atlases/AAL/AAL_116_2MM -o /data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_Parcellated_AAL_116_2MM -r /data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA.nii.gz -w /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv --postmat=/data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2FA.mat --interp=nn
** ERROR (nifti_image_read): failed to find header file for '/data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv'
** ERROR: nifti_image_open(/data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv): bad header info
ERROR: failed to open file /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv
ERROR: Could not open image /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv
Image Exception : #22 :: Failed to read volume /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv
An error occured while reading file: /data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152_warp_inv
** ERROR (nifti_image_read): failed to find header file for '/data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_Parcellated_AAL_116_2MM'
** ERROR: nifti_image_open(/data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_Parcellated_AAL_116_2MM): bad header info
ERROR: failed to open file /data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_Parcellated_AAL_116_2MM
Cannot open volume /data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_Parcellated_AAL_116_2MM for reading!
/data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_2T1

Finished. To view, point your web browser at
file:/data/fsl/projects/feye_dti/test/pat/00020/quality_control/FA_to_T1/slicesdir/index.html
/data/fsl/projects/feye_dti/test/pat/00020/native_space/volume0000_brain2_2MNI152

Finished. To view, point your web browser at
file:/data/fsl/projects/feye_dti/test/pat/00020/quality_control/T1_to_MNI152/slicesdir/index.html

****************
Checking outputs
****************
The output file or directory /data/fsl/projects/feye_dti/test/pat/00020/native_space/dti_00020_FA_Parcellated_AAL_116_2MM.nii.gz has not been generated!

************************************************
24-Aug-2012 14:13:06 : The job has FAILED
Total time used to process the job : 587.60 sec.
************************************************
Warning: File
'/data/fsl/projects/feye_dti/test/logs//PartitionTemplate2FA_00001.running'
not found.
> In psom_run_job at 178

ans =

     1