6 Jan
2018
6 Jan
'18
6:21 p.m.
Dear Antonin,
Thank you for your reply and clarification at https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-December/055331.h... . I was changing the recon-all file in the subject folder rather than the one in the freesurfer/bin folder. The command recon-all now runs to completion following your recommendations (replacing ln with cp, and making a local copy of fsaverage in the subject folder).
Many thanks once again!
Shadia
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-----Original Message-----
From: MIKHAEL Shadia
Sent: 31 December 2017 11:18
To: 'freesurfer@nmr.mgh.harvard.edu' freesurfer@nmr.mgh.harvard.edu
Subject: RE: FreeSurfer recon-all issue
Dear Antonin,
Thank you for your suggestions at https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-December/055319.h... . I've tried both, but the process still fails at the same point.
It appears that I now am left with a recon-all log file (attached) that is double in length (run 1 ending at line 4187, and run 2 ending at 8276), both of which have started from step 1, rather than run 2 resuming from where we last stopped.
Should I be adding certain flags for recon-all to resume rather than start from the beginning? The way I did it was the same as before, but without the -I flag in the second run, as suggested by the recon-all prompt.
Thanks again.
Shadia
-----Original Message-----
From: MIKHAEL Shadia
Sent: 28 December 2017 10:12
To: 'freesurfer@nmr.mgh.harvard.edu' freesurfer@nmr.mgh.harvard.edu
Subject: FreeSurfer recon-all issue
Hello all,
I'm having trouble with recon-all on a Linux server, I'm running into the following error for all of my subjects:
.....
mris_curvature -w lh.white.preaparc
total integrated curvature = 6.657*4pi (83.654) --> -6 handles ICI = 129.9, FI = 1309.2, variation=20703.115 writing Gaussian curvature to ./lh.white.preaparc.K...done.
writing mean curvature to ./lh.white.preaparc.H...done.
rm -f lh.white.H
ln -s lh.white.preaparc.H lh.white.H
ln: creating symbolic link `lh.white.H': Operation not supported Linux bsrv10 ..... #1 SMP Tue Nov 15 14:13:21 CST 2016 x86_64 x86_64 x86_64 GNU/Linux
I've tried to create a symbolic link as suggested in https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-September/040476... , but I still get a message saying operation not supported
ln -s /usr/local/freesurfer/subjects/fsaverage /home/s1163658/W/Cortical_analyses_for_ageing_and_dementia/NIH_Shadia
ln: creating symbolic link `/home/s1163658/W/Cortical_analyses_for_ageing_and_dementia/NIH_Shadia/fsaverage': Operation not supported
I've also tried to manually create the symbolic link in that last line: ln -s lh.white.preaparc.H lh.white.H But again it says operation not supported.
Recon-all log: attached
Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
Any advice?
Thank you
Shadia