Thank you again for the reply, Bruce!
After I typed: which mri_convert
It came up with: Desktop/freesurfer/bin/mri_convert
Let me know if any other info you need please. Thank you!
PS. I changed the subject of this email from the Digest to my original question-related one. Really sorry, but I'm still trying to figure out how to manage/operate with this mailing list.
-Abel (Chia-Ming) ________________________________________ ------------------------------
Message: 6 Date: Sat, 6 Sep 2014 16:02:05 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] about issues with "recon-all" To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1409061601220.23927@nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-1"
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:
- 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"
- 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
- 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
?
?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
------------------------------
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
End of Freesurfer Digest, Vol 127, Issue 8 ******************************************
then you type recon-all on the next line and it gives you all the command not found errors? On Sun, 7 Sep 2014, Lei, Chia-Ming wrote:
Thank you again for the reply, Bruce!
After I typed: which mri_convert
It came up with: Desktop/freesurfer/bin/mri_convert
Let me know if any other info you need please. Thank you!
PS. I changed the subject of this email from the Digest to my original question-related one. Really sorry, but I'm still trying to figure out how to manage/operate with this mailing list.
-Abel (Chia-Ming) ________________________________________
Message: 6 Date: Sat, 6 Sep 2014 16:02:05 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] about issues with "recon-all" To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1409061601220.23927@nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-1"
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:
- 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"
- 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
- 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
?
?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
End of Freesurfer Digest, Vol 127, Issue 8
Thank you for the response (again), Bruce!
If I type "recon-all" (only) right after the source command without setenv SUBJECTS_DIR, it gives me "USAGE: recon-all" with info of the whole recon-all process. I attached the whole message in the text file, recon-all without setenv SUBJECTS_DIR.
If I setenv SUBJECTS_DIR first by typing to indicate the folder where the .dcm files are: setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/Dickey-Pilot/003
and type the full recon-all command with: recon-all -i $SUBJECTS_DIR/003-0001-00003-0.dcm -s mike-dickey -all
then I get that long message saying many commands not found. I attached the message in the text file, recon-all with setenv SUBJECTS_DIR.
Let me know if any other info you need please. I appreciate your time greatly!
-Abel
On 09/07/2014 08:29 PM, Bruce Fischl wrote:
then you type recon-all on the next line and it gives you all the command not found errors? On Sun, 7 Sep 2014, Lei, Chia-Ming wrote:
Thank you again for the reply, Bruce!
After I typed: which mri_convert
It came up with: Desktop/freesurfer/bin/mri_convert
Let me know if any other info you need please. Thank you!
PS. I changed the subject of this email from the Digest to my original question-related one. Really sorry, but I'm still trying to figure out how to manage/operate with this mailing list.
-Abel (Chia-Ming) ________________________________________
Message: 6 Date: Sat, 6 Sep 2014 16:02:05 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] about issues with "recon-all" To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1409061601220.23927@nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-1"
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:
- 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"
- 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
- 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
?
?
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
End of Freesurfer Digest, Vol 127, Issue 8
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Abel,
Is this still an issue for you? If so please type the following 3 commands to the command terminal and send me the output.
Also, lets take this conversation offline, so please just send the output directly to my email address directly, not the list.
setenv FREESURFER_HOME Desktop/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh setenv SUBJECTS_DIR $FREESURFER_HOME
-Zeke
On 09/07/2014 08:59 PM, Abel Lei wrote:
Thank you for the response (again), Bruce!
If I type "recon-all" (only) right after the source command without setenv SUBJECTS_DIR, it gives me "USAGE: recon-all" with info of the whole recon-all process. I attached the whole message in the text file, recon-all without setenv SUBJECTS_DIR.
If I setenv SUBJECTS_DIR first by typing to indicate the folder where the .dcm files are: setenv SUBJECTS_DIR $FREESURFER_HOME/subjects/Dickey-Pilot/003
and type the full recon-all command with: recon-all -i $SUBJECTS_DIR/003-0001-00003-0.dcm -s mike-dickey -all
then I get that long message saying many commands not found. I attached the message in the text file, recon-all with setenv SUBJECTS_DIR.
Let me know if any other info you need please. I appreciate your time greatly!
-Abel
On 09/07/2014 08:29 PM, Bruce Fischl wrote:
then you type recon-all on the next line and it gives you all the command not found errors? On Sun, 7 Sep 2014, Lei, Chia-Ming wrote:
Thank you again for the reply, Bruce!
After I typed: which mri_convert
It came up with: Desktop/freesurfer/bin/mri_convert
Let me know if any other info you need please. Thank you!
PS. I changed the subject of this email from the Digest to my original question-related one. Really sorry, but I'm still trying to figure out how to manage/operate with this mailing list.
-Abel (Chia-Ming) ________________________________________
Message: 6 Date: Sat, 6 Sep 2014 16:02:05 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] about issues with "recon-all" To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.03.1409061601220.23927@nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-1"
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:
- 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"
- 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
- 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,
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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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End of Freesurfer Digest, Vol 127, Issue 8
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Abel Lei -
Bruce Fischl -
Lei, Chia-Ming
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Z K