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Hi Jim,
Sorry, I made a mistake going through recon-all process.
Your recon-all options '-autorecon2-noaseg -autorecon3' will start from recon-all stage 12 (Intensity Normalization 2). 'cortex.label' is regenerated. The updated stats files aseg.stats and ?h.aparc.stats incorporate any changes made.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Monday, July 10, 2023 11:44 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] re-running recon-all after aseg.presurf.mgz edits
External Email - Use Caution Thx for clarifying.
Can someone please clarify if ?h.aparc.stats and cortex.label are also regenerated?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Huang, Yujing Sent: Monday, July 03, 2023 11:24 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] re-running recon-all after aseg.presurf.mgz edits
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External Email - Use Caution With '-autorecon2-noaseg -autorecon3', I believe aseg.mgz is re-created. So, aseg.stats should reflect the changes.
I'm not sure cortex.label is re-created with these two options. So, not sure about ?h.aparc.stats.
Best,
Yujing
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Alexopoulos, Dimitrios Sent: Thursday, June 29, 2023 4:57 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] re-running recon-all after aseg.presurf.mgz edits
External Email - Use Caution A few quick questions FS experts.
I made manual edits on subcortical structures in outputs from FS6.0. Specifically, I made the edits on the aseg.presurf.mgz file. I then reran using: recon-all -s neo267e_nil -autorecon2-noaseg -autorecon3
Do the updated stats files aseg.stats and ?h.aparc.stats incorporate these changes?
I ask b/c the mri_segstats cmdline below uses the aseg.mgz not aseg.presurf.mgz
# Title Segmentation Statistics # # generating_program mri_segstats # cvs_version $Id: mri_segstats.c,v 1.121 2016/05/31 17:27:11 greve Exp $ # cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /usr/local/pkg/freesurfer6.0/ASegStatsLUT.txt --subject neo267f_nil
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