External Email - Use Caution
Dear FreeSurfer Develovers,
FreeSurfer 7.1 was recently installed on our cluster. I am testing it and stumbled on the error. It is difficult for me to debug it myself (perhaps if https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV7https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0.1 existed it would help me). I hope you can help.
The symptom is that I run:
recon-all -s FOLDER_1 -hemi lh -white -smooth2 -inflate2 -sphere -surfreg -cortparc -pial -sd FOLDER_2
Notice strange combination: -s FOLDER_1 -sd FOLDER_2 . Data is actually in FOLDER_2 where specific subject is set up in the environmental variable. The error message in recon-all.log is:
mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm
smoothing for 3 iterations setting seed for random number generator to 1234 error: No such file or directory error: MRISread(../surf/lh.white.preaparc): could not open file error: No such file or directory error: mris_smooth: could not read surface file ../surf/lh.white.preaparc
Indeed, file ../surf/lh.white.preaparc does not exist. It seems to indicate that -white was not actually executed before -smooth2. This command worked on version 6.0. Is this a bug in recon-all script version 7.1? Is this expected?
Previous successful command on the same data was:
recon-all -s FOLDER_1 -hemi lh -fix -sd FOLDER_2
General info:
1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b 2) Platform: likely CentOS, not sure how to tell 3) uname -a: Linux loginnode4 2.6.32-696.6.3.el6.694g0000.x86_64 #1 SMP Wed Jul 12 02:19:57 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: not attached because folder structure contains sensitive information that is hard to remove.
Thank you,
Roman