External Email - Use Caution
Hello All,
When running the longitudinal pipeline for version 6, i encountered this error " TransformSample: gcam has not been inverted!; Numerical result out of range". I found a thread with similar error but the problem wasn't solved. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-April/051240.html . Just like the previous thread, it happens whenever I include the "-bigventricle" flag. Below is a sample of my recon-all scripts from cross-sectional to longitudinal. The error.log and recon.log files are too large to send. Thank you.
Best, Paul
Cross-sectional recon-all -s ${SUBJECTS_DIR}/$session -autorecon-all -i ${filename} -hippocampal-subfields-T1 -parallel -openmp 20 -bigventricles -3T -time
Longitudinal recon-all -base ${session} -tp "${tp1}" -tp "${tp2}" -all -parallel -openmp 20 -bigventricles -3T -time
recon-all -long ${tp1} ${session} -all -parallel -openmp 20 -bigventricles -3T -time recon-all -long ${tp2} ${session} -all -parallel -openmp 20 -bigventricles -3T -time
External Email - Use Caution
Hello, Can anyone help me with this? I think it got lost in the pool of email.
Best, Paul ---------- Forwarded message ---------- From: miracle ozzoude miracooloz@gmail.com Date: Thu, Jul 5, 2018 at 12:23 PM Subject: error with mri_ca_register in long To: Douglas N Greve freesurfer@nmr.mgh.harvard.edu
Hello All,
When running the longitudinal pipeline for version 6, i encountered this error " TransformSample: gcam has not been inverted!; Numerical result out of range". I found a thread with similar error but the problem wasn't solved. https://mail.nmr.mgh.harvard.edu/pipermail/ freesurfer/2017-April/051240.html. Just like the previous thread, it happens whenever I include the "-bigventricle" flag. Below is a sample of my recon-all scripts from cross-sectional to longitudinal. The error.log and recon.log files are too large to send. Thank you.
Best, Paul
Cross-sectional recon-all -s ${SUBJECTS_DIR}/$session -autorecon-all -i ${filename} -hippocampal-subfields-T1 -parallel -openmp 20 -bigventricles -3T -time
Longitudinal recon-all -base ${session} -tp "${tp1}" -tp "${tp2}" -all -parallel -openmp 20 -bigventricles -3T -time
recon-all -long ${tp1} ${session} -all -parallel -openmp 20 -bigventricles -3T -time recon-all -long ${tp2} ${session} -all -parallel -openmp 20 -bigventricles -3T -time
Hi Paul,
Does this happen in the base or in the long step?
-bigventricle has never been tested within the long stream and this is bug that needs to be fixed at some point (assuming the big ventricle is supported in the next release )
We should put this on our known issues list.
Best, Martin
On 5. Jul 2018, at 18:23, miracle ozzoude miracooloz@gmail.com wrote:
External Email - Use CautionHello All,
When running the longitudinal pipeline for version 6, i encountered this error " TransformSample: gcam has not been inverted!; Numerical result out of range". I found a thread with similar error but the problem wasn't solved. https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-April/051240.html https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2017-April/051240.html. Just like the previous thread, it happens whenever I include the "-bigventricle" flag. Below is a sample of my recon-all scripts from cross-sectional to longitudinal. The error.log and recon.log files are too large to send. Thank you.
Best, Paul
Cross-sectional recon-all -s ${SUBJECTS_DIR}/$session -autorecon-all -i ${filename} -hippocampal-subfields-T1 -parallel -openmp 20 -bigventricles -3T -time
Longitudinal recon-all -base ${session} -tp "${tp1}" -tp "${tp2}" -all -parallel -openmp 20 -bigventricles -3T -time
recon-all -long ${tp1} ${session} -all -parallel -openmp 20 -bigventricles -3T -time recon-all -long ${tp2} ${session} -all -parallel -openmp 20 -bigventricles -3T -time _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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miracle ozzoude