External Email - Use Caution
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 wrote:
> External Email - Use Caution
>
> 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 <
> matthieuvanhou...@gmail.com> wrote:
>
>> External Email - Use Caution
>>
>> 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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--
Cassidy McDermott
Clinical Psychology Ph.D. Student
University of Pennsylvania | Changing Brain Lab
cass...@sas.upenn.edu | 425-274-5862
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