Dear Shadia,

please check, that you really edited your recon.all, as I suggested in my previous mail. Your recon-all file is located here: /home/s1163658/freesurferv60/bin/recon-all

According to your recon-all.log, there is still an ln -s command invoked (which should be replaced by cp command).

It is normal that the log from new invocation of recon-all is appended to current recon-all.log.

As a test, you can try to run only the step which is currently failing:

recon-all -s your_subject -curvHK

Also, by default, recon-all invocation does not automatically account already finished steps. To skip already successfully finished steps, you can try to run recon-all -s your_subject -make all (not sure if it works OK in v6)

or explicitly list steps which need to be run:

recon-all -s your_subject -curvHK -curvstats -autorecon3

Antonin

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

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-----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