Dear FreeSurfers,
I just recently installed FreeSurfer and as Saeed ( http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg49263.html) had troubles running recon-all.
My info: 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 2) Linux version: Linux unanderra 4.4.0-45-generic #66-Ubuntu SMP Wed Oct 19 14:12:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux
I attach my recon-all.log but I guess it is very similar to Saeed's. Also running
mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz
gives the exact output and error code as he had. I already read that downloading the Development Version should get the job done, but noticed some stuff and wanted to ask about it:
Running "recon-all -s bert -all" , the following lines are shown and the build stamps do not match.
INFO: FreeSurfer build stamps do not match Subject Stamp: freesurfer-Linux-centos4-stable-v5.3.0beta-20130503 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/bin/freesurfer/subjects Actual FREESURFER_HOME /usr/local/bin/freesurfer -rw-r--r-- 1 albert albert 513977 Oct 31 16:30 /usr/local/bin/freesurfer/subjects/bert/scripts/recon-all.log Linux unanderra 4.4.0-45-generic #66-Ubuntu SMP Wed Oct 19 14:12:37 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux INFO: current FREESURFER_HOME does not match that of previous processing. Current: /usr/local/bin/freesurfer Previous: /space/freesurfer/centos4.0/stable
Equally in the attached recon-all.log file "FREESURFER_HOME /space/freesurfer/centos4.0/stable Actual FREESURFER_HOME /autofs/cluster/freesurfer/centos4.0/stable5"
is written and although I downloaded the centos6-version and not the centos4.0 version. Might this be a problem or is the error solely due to the new perl versions? Just wanted to bring it to your attention and hear your feedback. I am currently downloading the 6.0.0-beta version, which hopefully makes recon-all work again.
Have a great day,
Albert