I ended up fixing the error through symlink.
________________________________ From: Rongxiang Tang rongxiangtang@yahoo.com To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, September 4, 2013 8:04 PM Subject: error during longitudinal -base stream
Hi All,
I found an error during the longitudinal -base stream:
#@# Ex-vivo Entorhinal Cortex Label lh Wed Sep 4 19:35:00 CDT 2013
mris_spherical_average -erode 1 -orig white -t 0.4 -o 611 label lh.entorhinal lh sphere.reg lh.EC_average lh.entorhinal_exvivo.label
painting output onto subject 611. processing subject lh.EC_average... MRISread(/mnt/fs1/work/results/lh.EC_average/surf/lh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Not a directory mris_spherical_average: could not read surface file /mnt/fs1/work/results/lh.EC_average/surf/lh.sphere.reg Not a directory
mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b -l ./lh.entorhinal_exvivo.label 611 lh white
limiting computations to label ./lh.entorhinal_exvivo.label. reading volume /mnt/fs1/work/results/611/mri/wm.mgz... reading input surface /mnt/fs1/work/results/611/surf/lh.white... reading input pial surface /mnt/fs1/work/results/611/surf/lh.pial... reading input white surface /mnt/fs1/work/results/611/surf/lh.white... INFO: assuming MGZ format for volumes. No such file or directory mris_anatomical_stats: could not open label file ./lh.entorhinal_exvivo.label No such file or directory 611: could not read label file (null)
No such file or directory #-------------------------------------------- #@# Ex-vivo Entorhinal Cortex Label rh Wed Sep 4 19:35:05 CDT 2013
mris_spherical_average -erode 1 -orig white -t 0.4 -o 611 label rh.entorhinal rh sphere.reg rh.EC_average rh.entorhinal_exvivo.label
painting output onto subject 611. processing subject rh.EC_average... MRISread(/mnt/fs1/work/results/rh.EC_average/surf/rh.sphere.reg): could not open file eroding label 1 times before writing thresholding label stat at 0.400 before writing Not a directory mris_spherical_average: could not read surface file /mnt/fs1/results/rh.EC_average/surf/rh.sphere.reg Not a directory
mris_anatomical_stats -mgz -f ../stats/rh.entorhinal_exvivo.stats -b -l ./rh.entorhinal_exvivo.label 611 rh white
limiting computations to label ./rh.entorhinal_exvivo.label. reading volume /mnt/fs1/work/results/611/mri/wm.mgz... reading input surface /mnt/fs1/work/results/611/surf/rh.white... reading input pial surface /mnt/fs1/work/results/611/surf/rh.pial... reading input white surface /mnt/fs1/work/results/611/surf/rh.white... INFO: assuming MGZ format for volumes. No such file or directory mris_anatomical_stats: could not open label file ./rh.entorhinal_exvivo.label No such file or directory 611: could not read label file (null)
No such file or directory
#------------------------------------------
Started at Wed Sep 4 10:22:15 CDT 2013 Ended at Wed Sep 4 19:35:10 CDT 2013 #@#%# recon-all-run-time-hours 9.215 recon-all -s 611 finished without error at Wed Sep 4 19:35:10 CDT 2013 done
although it tells me that the subject finished without error, clearly there is some error....does it affect my analysis or could I simply ignore it?
Thanks in advance, Catherine