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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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,

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_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

after you run the source command can you type:

which mri_convert

and let us know what it says? This is not a FreeSurfer issue - it's a problem with your path Bruce

On Sat, 6 Sep 2014, Lei, Chia-Ming wrote:

Thank you for the reply, Bruce. (Really sorry but I just changed my email address, so I decided to reply again with the currently subscribed email...)

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 (below attached) 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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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,

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_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

---

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