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