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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
