Hi Lucette

how do you do the editing? Looks like it was in some other package, which probably accounts for the error. You should be able to fix it by cding into the mri dir and running:

mri_convert -rt nearest -rl orig.mgz aseg.your_edits.mgz aseg.mgz

cheers Bruce

On Thu, 5 Jan 2017, Lucette Cysique wrote:

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

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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

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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