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thanks, the subj I sent you the logfile has a cut on the posterior part, I uploaded a similar case 098_S_4275_20181221.tar.gz

Is there any way to run gtmseg regardless?

Thanks

Am Fr., 5. Juni 2020 um 20:01 Uhr schrieb Douglas N. Greve <dgreve@mgh.harvard.edu>:

Hmmm, not sure what is going on here. I'm guessing that the back of the head was cut off (or wrapped around). Is that right? I'm not sure why this would create an error. If you upload one of your subjects, I'll take a look. See instructions below

From the linux command line,
Create the file you want to upload, eg,
cd $SUBJECTS_DIR
tar cvfz subject.tar.gz ./subject
Now log  into our anonymous FTP site:
ftp surfer.nmr.mgh.harvard.edu
It will ask you for a user name: use "anonymous" (no quotes)
It will ask you for a password: use "anonymous" (no quotes)
cd transfer/incoming
binary
put subject.tar.gz
Send an email that the file has been and the name of the file.

On 6/4/2020 9:40 AM, Boris Rauchmann wrote:

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Please find the logfile attached. 

Thank you

Am Do., 4. Juni 2020 um 15:18 Uhr schrieb Douglas N. Greve <dgreve@mgh.harvard.edu>:

Can you send the log file?

On 6/4/2020 9:12 AM, Boris Rauchmann wrote:

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Dear FS experts, 

In my dataset I have 4 subjects where the T1 was acquired, planning the FOV very close to the occipital lobe. I guess that triggers the error: getSignalBehindHead ERROR (no slices behind head) WARNING: only 0 < 7 slices behind head! ERROR: xcerebralseg  and results in gtmseg exited with errors.

How can I fix this?

Best regards,

Boris

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