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Martin,
That is the point. I have edited the hippocampus in the -long 2 times and the recon does not maintain my edits.
I would love any help to changes I should be making to my recon statement to maintain my edits.
Rebecca
Hi Rebecca,
aseg edits to subcortical structures need to be done in the -long stage. (see here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdits ) Best, Martin
On Thu, 2018-09-06 at 14:37 -0700, Rebecca Ray wrote:
External Email - Use Caution
*>* HELP *>* ---------- Forwarded message ---------- *>* From: Rebecca Ray <rayr5 at gene.com https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> *>* Date: Thu, Sep 6, 2018 at 12:05 PM *>* Subject: longitudinal hippocampal aseg editing *>* To: freesurfer at nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer *> > >* I have 2 time points on 60 subjects with most being in some form of *>* AD. There are considerable differences in hippocampal volume between *>* time points. I edited the raw images before making the template. I *>* then had to edit the aseg template image and there were still *>* problems on the -long images. I tried to edit and rerun autorecon2- *>* noaseg and autorecon3 and it does not appear to be keeping my edits. *> >* What am I doing wrong? *> >* Rebecca *> >* _______________*
Hi Rebecca,
I see. Generally, it should behave in the same way as cross sectional processing:
If both aseg.mgz and aseg.auto.mgz exist, and they are different, then the file aseg.manedit.mgz is created from the differences (and if an aseg.manedit.mgz file also exists, then its contents are merged with the newly created aseg.manedit.mgz). If aseg.manedit.mgz exists, then its contents are merged with aseg.auto.mgz (which is the output of the automatic segmentation program mri_ca_label). The default action, if neither aseg.manedit.mgz nor aseg.mgz exist, is to copy aseg.auto.mgz to aseg.mgz.
Can you check (with a simple edit) in a cross sectional run, if it behaves as expected, then check what happens in the long if you do the same steps? Could be that there is a bug in the code for -long processing, but not sure.
Best, Martin
On Fri, 2018-09-07 at 09:55 -0700, Rebecca Ray wrote:
External Email - Use Caution Martin, That is the point. I have edited the hippocampus in the -long 2 times and the recon does not maintain my edits. I would love any help to changes I should be making to my recon statement to maintain my edits.
Rebecca
Hi Rebecca,
aseg edits to subcortical structures need to be done in the -long stage. (see here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalEdit s ) Best, Martin
On Thu, 2018-09-06 at 14:37 -0700, Rebecca Ray wrote:
External Email - Use Caution HELP ---------- Forwarded message ---------- From: Rebecca Ray <rayr5 at gene.com> Date: Thu, Sep 6, 2018 at 12:05 PM Subject: longitudinal hippocampal aseg editing To: freesurfer at nmr.mgh.harvard.edu I have 2 time points on 60 subjects with most being in some form of AD. There are considerable differences in hippocampal volume
between
time points. I edited the raw images before making the template. I then had to edit the aseg template image and there were still problems on the -long images. I tried to edit and rerun
autorecon2-
noaseg and autorecon3 and it does not appear to be keeping my
edits.
What am I doing wrong? Rebecca _______________
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Rebecca Ray