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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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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.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Thursday, June 29, 2023 4:57 PM To: 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
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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Thx for clarifying.
Can someone please clarify if ?h.aparc.stats and cortex.label are also regenerated?
Jim
From: freesurfer-bounces@nmr.mgh.harvard.edu 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.edu Subject: Re: [Freesurfer] re-running recon-all after aseg.presurf.mgz edits
* External Email - Caution *
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
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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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
* External Email - Caution *
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
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
freesurfer@nmr.mgh.harvard.edu
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Alexopoulos, Dimitrios -
Huang, Yujing