Hi Matthew
where are the dicoms located? Does that file exist? What happens if you do:
ls -l /home/mclem/freesurfer/testsubjects/0000142/000001.dcm
cheers Bruce On Fri, 11 Jul 2014, Matthew Clem wrote:
Hi FreeSurfers,
I am very new to FreeSurfer and I'm having some issues uploading my first subject. I have a subject folder with 160 .dcm files and FreeSurfer cannot find the files.
Here is the script I used:
recon-all -s 0000142 \ -i $SUBJECTS_DIR/0000142/000001.dcm
I even tried to type out the full path instead of using $SUBJECTS_DIR variable and cd to where the files are stored and it still didn't work.
Here is my output:
ERROR: cannot find /home/mclem/freesurfer/testsubjects/0000142/000001.dcm Linux ubuntu 3.13.0-24-generic #46-Ubuntu SMP Thu Apr 10 19:11:08 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 0000142 exited with ERRORS at Fri Jul 11 15:27:34 CDT 2014
Any thoughts on what I'm doing wrong?
Thanks,
Matthew Clem, M.Ed. Doctoral Student Clinical Psychology UT Southwestern Medical Center Matthew.Clem@utsouthwestern.edu
UT Southwestern Medical Center The future of medicine, today.