Hi,

I’m also encountering a similar issue. I am using Freesurfer 6.0.0 with the new recon-all.makefile copied in. After completing manual edits, I re-ran the recon with the -make all flag. The recon-all.log for this subject indicates that the recon finished without error. However, the qsub job log file for the same recon has “ERROR: Flag -ccseg unrecognized.” Do you know what causes this error? And why might the error show up in the job log but not the recon log?

Thank you,

Cassidy

On Fri, Jun 19, 2020 at 4:16 AM Niels Bergsland <theniels@gmail.com> wrote:

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Hi all,
Just following up on this as I've run into the exact same problem. Is there a different recon-all.makefile that should be used for FS 6/6.0.1 ?

Thanks!

On Fri, Mar 29, 2019 at 9:28 AM Matthieu VANHOUTTE <matthieuvanhoutte@gmail.com> wrote:

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Dear Freesurfer's experts,

Havng done multiple types of manual editing in two subjects, I relaunched the recon-all process (Freesurfer 6.0.1) with the flag "-make all".

However, during the process, I goth for both subjects the following error message:

make: *** [/netapp/vol2_agewell/pro/IMAP/imap_mvh/FS6.0.1/awellv1s097/mri/aseg.presurf.mgz] Error 1

recon-all -s /netapp/vol2_agewell/pro/IMAP/imap_mvh/FS6.0.1/awellv3s024 -ccseg
ERROR: Flag -ccseg unrecognized.

Following the troubleshooting site (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingDataV6.0) I have over-writed the "recon-all.makefile" file since I use the 6.0.1 version of Freesurfer.

Thanks for helping.

Best,

Matthieu

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