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