Hi Can

it looks like the partition you were writing the results to was full. Can you check? Or possibly you don't have gzip on your system?

cheers Bruce On Wed, 7 Sep 2011, can at?lgan wrote:

Hello,

Firstly, I'm new to FreeSurfer. My objective is to get a thickness map of cerebral cortex. I converted a single slice of T1 dicom series in order to see whether i could get a proper result. I started the reconstruction progress simply with : recon-all -s 001 -all but after a long period of time the progress halted with a couple of error messages :

---------- unfolding failed - restoring original position -------------------- 0637: dt=0.000078, rms=0.365 (0.000%), neg=0, invalid=766 GCAMwrite(transforms/talairach.m3z): gzip encountered error. writing output transformation to transforms/talairach.m3z... GCAMwrite GCAMwrite:: m3z loop GCAMwrite:: the command is:  gzip -f -c > transforms/talairach.m3z GCAMwrite:: the popen error code is:  12 mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed ERROR: mri_ca_register with non-zero status 252 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Wed Sep  7 06:14:11 EEST 2011 /home/socat/Desktop/can/001/mri

mri_ca_register -invert-and-save transforms/talairach.m3z

Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux hstkaddogpc-160-75.ege.edu.tr 2.6.9-55.ELsmp #1 SMP Fri Apr 20 17:03:35 EDT 2007 i686 i686 i386 GNU/Linux

recon-all -s 001 exited with ERRORS at Wed Sep  7 06:14:12 EEST 2011

before the error messages showed up that "ulfolding failed - restoring original position" steps were repeated 3 times.

About result evaluation; I digged through fs wiki to find out how i can get a visual cortical thickness map but I couldn't find anything but only average thickness value using mris_anatomical_stats command. How can I see such a map for example of sample data "bert"?

Thanks in advance. Regards, Can