Dear Antonin, Thank you for your reply and clarification at https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-December/055331.html . 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 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. -----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.html . 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.html , 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
