Hi FreeSurfers,
I’m a very beginner to both the Linux OS and the FreeSurfer program. After finally setting up the FreeSurfer, I was trying to do recon-all for my trial subject. But when I ran the “recon-all” command, it returned with a long error message indicating many commands not found. The message is copied and pasted below. I also attached the recon-all.log and recon-all.error in this email, which (probably) contains two failed attempts of the same command. Please let me know if you need any other info from me. I appreciate your help and time greatly! Thank you so much!
Chia-Ming (Abel) Lei
PhD Student/Graduate Student Researcher
Language and Brain Lab (LABlab) & Adult Language Lab
Department of Communication Sciences and Disorders
School of Health and Rehabilitation Science
University of Pittsburgh
-----below is the long~ error message------ chiaming-PORTEGE-R835:~> recon-all -all -s mike_dickeySubject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot Actual FREESURFER_HOME /home/chia-ming/Desktop/freesurfer -rw-rw-r-- 1 chia-ming chia-ming 2119 Sep 6 01:34 /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/scripts/recon-all.log Linux chiaming-PORTEGE-R835 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux mri_motion_correct.fsl: Command not found. talairach_avi: Command not found. tkregister2_cmdl: Command not found. nu_correct: Command not found. mri_make_uchar: Command not found. mri_normalize: Command not found. mri_watershed: Command not found. mri_gcut: Command not found. mri_segment: Command not found. mri_label2label: Command not found. mri_em_register: Command not found. mri_ca_normalize: Command not found. mri_ca_register: Command not found. mri_ca_label: Command not found. mri_pretess: Command not found. mri_fill: Command not found. mri_tessellate: Command not found. mri_concatenate_lta: Command not found. mri_normalize_tp2: Command not found. mris_smooth: Command not found. mris_inflate: Command not found. mris_curvature: Command not found. mris_sphere: Command not found. mris_fix_topology: Command not found. mris_topo_fixer: Command not found. mris_ca_label: Command not found. mris_euler_number: Command not found. mris_make_surfaces: Command not found. mris_register: Command not found. mris_volmask: Command not found. mris_anatomical_stats: Command not found. mrisp_paint: Command not found. mris_curvature_stats: Command not found. mris_calc: Command not found. mri_robust_register: Command not found. mri_robust_template: Command not found. mri_and: Command not found. mri_or: Command not found. mri_fuse_segmentations: Command not found. mri_segstats: Command not found. cp: cannot stat 'Desktop/freesurfer/bin/recon-all': No such file or directory #-------------------------------------------- #@# MotionCor Sat Sep 6 01:40:13 EDT 2014 ERROR: no run data found in /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/mri. Make sure to have a volume called 001.mgz in /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/mri/orig. If you have a second run of data call it 002.mgz, etc. See also: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Conversion Linux chiaming-PORTEGE-R835 3.13.0-35-generic #62-Ubuntu SMP Fri Aug 15 01:58:42 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s mike_dickey exited with ERRORS at Sat Sep 6 01:40:13 EDT 2014
For more details, see the log file /home/chia-ming/Desktop/freesurfer/subjects/Dickey-Pilot/mike_dickey/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting