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
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