Thank you for the reply, Bruce. I'm running on Linux 3.13.0-35-generic with Ubuntu 14.04. I couldn't set up the permanent shell switched to .tcsh, i.e. when I opened a new terminal, nothing happened. So I deleted the .tcsh file I created and manually input the following steps when I opened a terminal:
1. setenv FREESURFER_HOME Desktop/freesurfer 2. source $FREESURFER_HOME/SetupFreeSurfer.csh *note: the following message shows up withe the source command, "-------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME Desktop/freesurfer FSFAST_HOME Desktop/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR Desktop/freesurfer/subjects MNI_DIR Desktop/freesurfer/mni" 3. setenv SUBJECTS_DIR $FREESURFER_HOME/subjects *note: I also tried to set SUBJECTS_DIR to the specific folder where the .dcm files are. 3.1 setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/Dickey-Pilot/003 4. recon-all -i $SUBJECTS_DIR/Dickey-Pilot/003/003-0001-00003-0.dcm -s mike-dickey -all *OR 4.1 recon-all -i $SUBJECTS_DIR/003-0001-00003-0.dcm -s mike-dickey -all Then the long error message pasted in the first email showed up. Please let me know if any other info you need to figure out the issue is. Again, thank you so much for your help! -Abel -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Saturday, September 6, 2014 9:56 AM To: Freesurfer support list Subject: Re: [Freesurfer] about issues with "recon-all" Hi Abel what OS are you running on? Did you source the file $FREESURFER_HOME/FreeSurferEnv.csh ? cheers Bruce On Sat, 6 Sep 2014, Abel Lei wrote: > > Hi FreeSurfers, > > > > Im 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_dic > key/script > s/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/m > ri/or > ig. > 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_dick > ey/script > s/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > _______________________________________________ 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. 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