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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
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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:
External Email - Use CautionDear 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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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:
External Email - Use Caution
Please find the logfile attached.
Thank you
Am Do., 4. Juni 2020 um 15:18 Uhr schrieb Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
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:
External Email - Use CautionPlease 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:
External Email - Use CautionDear 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
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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:
External Email - Use Caution
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 mailto: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 <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:External Email - Use Caution Please find the logfile attached. Thank you Am Do., 4. Juni 2020 um 15:18 Uhr schrieb Douglas N. Greve <dgreve@mgh.harvard.edu <mailto:dgreve@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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Boris Rauchmann -
Douglas N. Greve