Hi Greg,

Thanks for your note. I actually got rid of the perl script already so in 5.1 it should not be a problem any more.

Lilla

On Thu, 19 May 2011, GREGORY R KIRK wrote:

running mri_cvs_register --mov 004 --template 003

get error executing surf2vol at /apps/x86_64_sci5/freesurfer-latest/bin/elastic_registration_CVS.pl line 162.

line 162 is system($cmdLine)==0 or die "error executing surf2vol";

i saw martin kavec posted the same error but did not see a response ' the command is $cmdLine is

surf2vol -fixed_mri /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/mri/norm.mgz -moving_mri /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/mri/norm.mgz -fixed_surf /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/surf/lh.white -moving_surf /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/lh.resample.white -fixed_surf_2 /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/surf/rh.white -moving_surf_2 /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/rh.resample.white -fixed_surf_3 /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/surf/lh.pial -moving_surf_3 /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/lh.resample.pial -fixed_surf_4 /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/surf/rh.pial -moving_surf_4 /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/rh.resample.pial -aparc /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/label/lh.aparc.annot -aparc_2 /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/label/rh.aparc.annot -aparc_3 /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/label/lh.aparc.annot -aparc_4 /study5/aa-scratch/TEENEMO/freesurfer_subjects/003/label/rh.aparc.annot -lin_res 20 -ksp_rtol 1.0e-9 -cache_transform /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/transform.txt -penalty_weight 1000 -fem_steps 17 -elt_vol_range 5.0,10.0 -log_summary -poisson .3 -topology_old -compress -pc_type none -ksp_type preonly -pc_type jacobi -ksp_type cg -ksp_view -ksp_converged_reason -out /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/el_reg_to003.mgz -out_surf /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/surf-mfc_to003 -out_mesh /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/el_reg_to003 &> /study5/aa-scratch/TEENEMO/freesurfer_subjects/004/cvs/trace_el_reg_to003_004.txt

if you cut and paste this in your freesurfer SUBJECTS_DIR it runs fine

but executing strace -f -o /scratch/trace.foo mri_cvs_register --mov 004 --template 003 --step2

one of the output lines is 16837 open("iteration.node", O_WRONLY|O_CREAT|O_TRUNC, 0666) = -1 EROFS (Read-only file system)

on another computer where i have freesurfer installed in my home directory the program runs fine.

so it seems that when the perl script executes the command and freesurfer is installed in a system directory like /usr/bin/... that the perl script home dir at the point of the system call is in the system directory and it is trying to write there rather than somewhere in SUBJECTS_DIR or other user writable location and surf2vol fails when it tries to open a file in write mode in a system directory

greg

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