Please could someone consider my email question sent dec 14th? Email below Thanks
Lucette A. Cysique, Ph.D.
NHMRC Clinical Career Development Fellow / UNSW Medicine 2013-2017 NeuroHIV and Quantitative Neuropsychology Group Leader @ NeuRA Senior Lecturer SoMs, UNSW Medicine Affiliated senior researcher at the St. Vincent's Hospital Sydney, Applied Medical Research Centre, Peter Duncan Neuroscience Unit
Postal Address: Neuroscience Research Australia PO Box 1165 (Street Address: 139 Barker Street) Randwick NSW 2031 Australia
Office Ph: +61 2 9399 1880 Mobile Ph: (+61) (0)431 576 710 (text preferred)
Emails: lcysique@unsw.edu.au (primary) Lucette.Cysique@svha.org.au (St. Vincent's Hospital Sydney, related project) lcysique@ucsd.edu (HIV Neurobehavioral Research Center/UCSD related project) Twitter: @Lucette_C http://www.neura.edu.au/research/themes/cysique-group ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lucette Cysique Sent: Monday, December 19, 2016 12:37:13 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Madeleine Nichols (Redirection) Subject: Re: [Freesurfer] minor edits to aseg lead to exist with errors in about 25% of my scans
sending this again as I have had no responses
Thanks
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Lucette Cysique Sent: Wednesday, December 14, 2016 12:52:11 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Madeleine Nichols (Redirection) Subject: [Freesurfer] minor edits to aseg lead to exist with errors in about 25% of my scans
Dear FS Wiki
I run my scan in FS without any problem
example:
#@#%# recon-all-run-time-hours 8.342
recon-all -s 877 finished without error
then I do some edits to the aseg in freeview
edits include: relabelling correctly lateral ventricles voxels mostly in the posterior horn of the lateral ventricles; white matter hyperintensities around those voxels which are erroneously considered as cortex also more often in the posterior horn of the lateral ventricles; and correcting erroneous allocation of choroid plexus also typically in the posterior horn of the lateral ventricles
Once done, I re-run using
recon-all -s $i -autorecon2-noaseg
example:
/mridata/workingdata/HIV/subjects/877
/usr/local/FREESURFER/freesurfer5.3.0/bin/recon-all
-s 877 -autorecon2-noaseg
in 25% of cases, I get the following error message and the process exists
example:
#--------------------------------------------
#@# Intensity Normalization2 Wed Dec 14 12:33:54 AEDT 2016
/mridata/workingdata/HIV/subjects/011/mri
mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
mri_normalize: aseg volume aseg.mgz must be conformed
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading from norm.mgz...
Reading aseg aseg.mgz
Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s 011 exited with ERRORS at Wed Dec 14 12:33:56 AEDT 2016
in the other no problem
example:
#@#%# recon-all-run-time-hours 1.116
recon-all -s 877 finished without error at Thu Dec 1 14:42:27 AEDT 2016