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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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