Get a new version of mri_seghead from here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_seghead
and copy it into $FREESURFER_HOME/bin
let me know if it works
On 6/5/2020 5:09 PM, Boris Rauchmann wrote:
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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
<dgr...@mgh.harvard.edu <mailto:dgr...@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 <http://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
<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>:
Can you send the log file?
On 6/4/2020 9:12 AM, Boris Rauchmann wrote:
External Email - Use Caution
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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