I recently downloaded and installed fs4v03 (CentOS 4x86_64) on my new 64bit linux box running RHEL 5 (Tikanga). I didn't see any special notes on the download page for RHEL 5 (only RHEL 4 is noted).
While test-driving my first dataset through the fsv403 pipeline, I encountered some difficulties with my explorations of the new feature of calculated local gyrification index. I tried the following cmd lines...each yielded the same standard out message pasted below
Any ideas? Jenifer
[jjuranek@localhost subjects]$ recon-all -subjid SB_09_H20089 -localGI [jjuranek@localhost subjects]$ recon-all -lgi -s SB_09_H20089 [jjuranek@localhost subjects]$ recon-all -lgi -sid SB_09_H20089
[jjuranek@localhost subjects]$ recon-all -lgi -s SB_09_H20089 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 jjuranek jjuranek 768975 Apr 18 17:30 /usr/local/freesurfer/subjects/SB_09_H20089/scripts/recon-all.log Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/SB_09_H20089/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Apr 18 17:45:32 CDT 2008
mris_compute_lgi --i lh.pial
Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Fri Apr 18 17:45:32 CDT 2008
Jenifer,
The new -localGI feature makes use of the pial surfaces that the freesurfer processing stream produces, so it is necessary for those to exist first. You can accomplish either with:
recon-all -s <subjid> -all
and inspect the surfaces, and then:
recon-all -s <subjid> -localGI
or in one step with:
recon-all -s <subjid> -all -localGI
although in this latter case, you would want to inspect the pial surface, as per the normal freesurfer procedure, to ensure that the localGI results are valid.
I need to update the wiki page, and recon-all error messages, to make this clearer.
Nick
On Fri, 2008-04-18 at 18:06 -0500, Juranek, Jenifer wrote:
I recently downloaded and installed fs4v03 (CentOS 4x86_64) on my new 64bit linux box running RHEL 5 (Tikanga). I didn't see any special notes on the download page for RHEL 5 (only RHEL 4 is noted).
While test-driving my first dataset through the fsv403 pipeline, I encountered some difficulties with my explorations of the new feature of calculated local gyrification index. I tried the following cmd lines...each yielded the same standard out message pasted below
Any ideas? Jenifer
[jjuranek@localhost subjects]$ recon-all -subjid SB_09_H20089 -localGI [jjuranek@localhost subjects]$ recon-all -lgi -s SB_09_H20089 [jjuranek@localhost subjects]$ recon-all -lgi -sid SB_09_H20089
[jjuranek@localhost subjects]$ recon-all -lgi -s SB_09_H20089 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 jjuranek jjuranek 768975 Apr 18 17:30 /usr/local/freesurfer/subjects/SB_09_H20089/scripts/recon-all.log Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/SB_09_H20089/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Apr 18 17:45:32 CDT 2008
mris_compute_lgi --i lh.pial
Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Fri Apr 18 17:45:32 CDT 2008
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Jenifer,
Have you installed Matlab on your computer? As far as I see it, either you don't have matlab, or the path to matlab is not set properly.
You can cd into the surf directory (cd SB_09_H20089/surf) and try directly: mris_compute_lgi --debug --i lh.pial
If it finishes in a few seconds with "getmatlab", then you have to add the matlab directory to you $PATH environment variable.
Marie
Quoting "Juranek, Jenifer " Jenifer.Juranek@uth.tmc.edu:
I recently downloaded and installed fs4v03 (CentOS 4x86_64) on my new 64bit linux box running RHEL 5 (Tikanga). I didn't see any special notes on the download page for RHEL 5 (only RHEL 4 is noted).
While test-driving my first dataset through the fsv403 pipeline, I encountered some difficulties with my explorations of the new feature of calculated local gyrification index. I tried the following cmd lines...each yielded the same standard out message pasted below
Any ideas? Jenifer
[jjuranek@localhost subjects]$ recon-all -subjid SB_09_H20089 -localGI [jjuranek@localhost subjects]$ recon-all -lgi -s SB_09_H20089 [jjuranek@localhost subjects]$ recon-all -lgi -sid SB_09_H20089
[jjuranek@localhost subjects]$ recon-all -lgi -s SB_09_H20089 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 jjuranek jjuranek 768975 Apr 18 17:30 /usr/local/freesurfer/subjects/SB_09_H20089/scripts/recon-all.log Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/SB_09_H20089/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Apr 18 17:45:32 CDT 2008
mris_compute_lgi --i lh.pial
Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Fri Apr 18 17:45:32 CDT 2008
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Marie, Thanks so much for your suggestion. You see it perfectly. I did not realize that matlab functionality was required to run lgi. Which essential components of matlab are suggested so that I may purchase the proper license(s)?
Jenifer ________________________________
From: Marie Schaer [mailto:Marie.Schaer@medecine.unige.ch] Sent: Sat 4/19/2008 7:44 AM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] LGI: EXITS with ERRORS
Jenifer,
Have you installed Matlab on your computer? As far as I see it, either you don't have matlab, or the path to matlab is not set properly.
You can cd into the surf directory (cd SB_09_H20089/surf) and try directly: mris_compute_lgi --debug --i lh.pial
If it finishes in a few seconds with "getmatlab", then you have to add the matlab directory to you $PATH environment variable.
Marie
Quoting "Juranek, Jenifer " Jenifer.Juranek@uth.tmc.edu:
I recently downloaded and installed fs4v03 (CentOS 4x86_64) on my new 64bit linux box running RHEL 5 (Tikanga). I didn't see any special notes on the download page for RHEL 5 (only RHEL 4 is noted).
While test-driving my first dataset through the fsv403 pipeline, I encountered some difficulties with my explorations of the new feature of calculated local gyrification index. I tried the following cmd lines...each yielded the same standard out message pasted below
Any ideas? Jenifer
[jjuranek@localhost subjects]$ recon-all -subjid SB_09_H20089 -localGI [jjuranek@localhost subjects]$ recon-all -lgi -s SB_09_H20089 [jjuranek@localhost subjects]$ recon-all -lgi -sid SB_09_H20089
[jjuranek@localhost subjects]$ recon-all -lgi -s SB_09_H20089 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 jjuranek jjuranek 768975 Apr 18 17:30 /usr/local/freesurfer/subjects/SB_09_H20089/scripts/recon-all.log Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/SB_09_H20089/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Apr 18 17:45:32 CDT 2008
mris_compute_lgi --i lh.pial
Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Fri Apr 18 17:45:32 CDT 2008
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Jenifer,
If I am not wrong (because most of the academic licences include all toolboxes), you will only need the "Image Processing Toolbox" which is used to create the outer surface. Otherwise, a basic installation should be fine.
Marie
Quoting "Juranek, Jenifer " Jenifer.Juranek@uth.tmc.edu:
Marie, Thanks so much for your suggestion. You see it perfectly. I did not realize that matlab functionality was required to run lgi. Which essential components of matlab are suggested so that I may purchase the proper license(s)?
Jenifer ________________________________
From: Marie Schaer [mailto:Marie.Schaer@medecine.unige.ch] Sent: Sat 4/19/2008 7:44 AM To: Juranek, Jenifer Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] LGI: EXITS with ERRORS
Jenifer,
Have you installed Matlab on your computer? As far as I see it, either you don't have matlab, or the path to matlab is not set properly.
You can cd into the surf directory (cd SB_09_H20089/surf) and try directly: mris_compute_lgi --debug --i lh.pial
If it finishes in a few seconds with "getmatlab", then you have to add the matlab directory to you $PATH environment variable.
Marie
Quoting "Juranek, Jenifer " Jenifer.Juranek@uth.tmc.edu:
I recently downloaded and installed fs4v03 (CentOS 4x86_64) on my new 64bit linux box running RHEL 5 (Tikanga). I didn't see any special notes on the download page for RHEL 5 (only RHEL 4 is noted).
While test-driving my first dataset through the fsv403 pipeline, I encountered some difficulties with my explorations of the new feature of calculated local gyrification index. I tried the following cmd lines...each yielded the same standard out message pasted below
Any ideas? Jenifer
[jjuranek@localhost subjects]$ recon-all -subjid SB_09_H20089 -localGI [jjuranek@localhost subjects]$ recon-all -lgi -s SB_09_H20089 [jjuranek@localhost subjects]$ recon-all -lgi -sid SB_09_H20089
[jjuranek@localhost subjects]$ recon-all -lgi -s SB_09_H20089 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer -rw-rw-r-- 1 jjuranek jjuranek 768975 Apr 18 17:30 /usr/local/freesurfer/subjects/SB_09_H20089/scripts/recon-all.log Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/SB_09_H20089/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Apr 18 17:45:32 CDT 2008
mris_compute_lgi --i lh.pial
Linux localhost.localdomain 2.6.18-8.el5 #1 SMP Fri Jan 26 14:15:14 EST 2007 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Fri Apr 18 17:45:32 CDT 2008
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Juranek, Jenifer -
Marie Schaer -
Nick Schmansky