Re: [Freesurfer] where to start recon-all after edits
Hi, If the surfaces are 'done' and we update/edit the the aseg.mgz with recon-all -surfsegedit and then run recon-all -autorecon2-cp -autorecon3 to update the .stats, this also creates new wm and pial surfaces that may be different to those used for -surfsegedit. Is that right? As another alternative, could we run say, recon-all -autorecon2-cp_ -autorecon3_ that have set DoWhiteSurfs = 0; set DoPialSurfs = 0; so that new surfaces are not created and avoid needing to recheck the wm/pial surfaces (as they were previously considered done) as well as being the same as those used for the -surfsegedit. Looking forward to a reply, thanks, P On Mon, 18 May 2015 16:27:31 -0700 prasser lt;pras...@zoho.comgt; wrote Hi, This is a repost, hope someone can please comment? Thanks. On Wed, 06 May 2015 00:07:17 -0700 prasser lt;pras...@zoho.comgt; wrote Thanks Martin. The concern I have with using -autorecon2-cp -autorecon3 after -surfsegedit is that, new surfaces are created during -autorecon2-cp -autorecon3 so that aseg and the surfaces are always out of step with each other. Any suggestions on how I could test the validity of the method described here as an alternative: recon-all -surfsegedit then edit aseg if needed and then: recon-all -aparc2aseg -segstats -wmparc On Tue, 05 May 2015 07:09:48 -0700 Martin Reuter lt;mreu...@nmr.mgh.harvard.edugt; wrote Yes, if this is in the long, you also need to add the -long …. stuff Martin On Apr 28, 2015, at 12:46 AM, prasser lt;pras...@zoho.comgt; wrote: Thanks for your response, not sure if I've quite got it yet. So, after the surfaces are done and we update/edit the the aseg.mgz with say, recon-all -surfsegedit we need to re-run recon-all -autorecon2-cp -autorecon3 On Thu, 23 Apr 2015 06:45:00 -0700 Bruce Fischl lt;fis...@nmr.mgh.harvard.edugt; wrote I would think autorecon2-cp autorecon3 would be fine, but maybe Martin can comment? On Wed, 22 Apr 2015, prasser wrote: gt; Repost.Thanks. gt; gt; gt; On Mon, 20 Apr 2015 16:35:29 -0700 lt;pras...@zoho.comgt; wrote gt; gt; Thank you again for your reply. gt; gt; For editing aseg.mgz, as mentioned in gt; gt; https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegme gt; ntations gt; gt; it does suggest using -autorecon2-noaseg, but from what I can see this does not gt; update the aparc+aseg.mgz and associated .stats etc is that correct? Doesn't gt; this command (as does -autorecon3) also re-create surfaces that would need to be gt; re-checked and re-edited if needed? gt; gt; Also, I think FS5.1 does not have the -autorecon2-noaseg flag. gt; gt; As an alternative, with completed wm/pial boundaries could we run gt; gt; recon-all -surfsegedit, gt; gt; then we would edit aseg as needed and then: gt; gt; recon-all -aparc2aseg -segstats -wmparc gt; gt; This will not change any surfaces but would update aseg.stats gt; aparc.a2009s+aseg.mgz wmparc.mgz wmparc.stats etc gt; gt; P gt; gt; gt; On Mon, 20 Apr 2015 13:42:49 -0700 Martin gt; Reuterlt;mreu...@nmr.mgh.harvard.edugt; wrote gt; Hi gt; gt; so take a look at gt; https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData gt; where the entry points are described ( for brainmask and finalsurfs gt; -autorecon-pial should be OK, for aseg it says to use gt; gt; -autorecon2-noaseg ) gt; Also this page gt; https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags gt; has details on the steps. gt; gt; Best, Martin gt; gt; gt; gt; On 04/20/2015 03:21 PM, Martin Reuter wrote: gt; gt; usually edits to surfaces should not be required in the long. The gt; surfaces there get initialized from the base, so you need to make gt; sure the base surface is as accurate as possible. Several edits also gt; get transferred automatically from the cross sectional runs. See gt; this gt; http://freesurfer.net/fswiki/LongitudinalEdits gt; for a description of the different edits, and where they should be gt; done. gt; gt; About where to restart after making the edits, everything should be gt; done the same way as in the regular (cross sectional) processing. gt; So you specifically ask about: gt; - brainmask edits gt; - brainfinalsurf edits gt; - and manual aseg edits. gt; gt; I just looked at the description of those regular edits gt; http://freesurfer.net/fswiki/Edits gt; but sadly there it does not say where to start re-run either. I'll gt; try to find out and update that soon. gt; gt; I hope someone with editing experience can chime in and tell us. (I gt; changed the subject, so that it get's read). gt; gt; Cheers, Martin gt; gt; On 04/20/2015 09:44 AM, Bruce Fischl wrote: gt; gt; cheers gt; Bruce gt; gt; gt; On Mon, 20 Apr 2015, prasser wrote: gt; gt; Dear All, gt; I wanted to check that corrections to a Long pial gt;
Re: [Freesurfer] where to start recon-all after edits
Hi, This is a repost, hope someone can please comment? Thanks. On Wed, 06 May 2015 00:07:17 -0700 prasser lt;pras...@zoho.comgt; wrote Thanks Martin. The concern I have with using -autorecon2-cp -autorecon3 after -surfsegedit is that, new surfaces are created during -autorecon2-cp -autorecon3 so that aseg and the surfaces are always out of step with each other. Any suggestions on how I could test the validity of the method described here as an alternative: recon-all -surfsegedit then edit aseg if needed and then: recon-all -aparc2aseg -segstats -wmparc On Tue, 05 May 2015 07:09:48 -0700 Martin Reuter lt;mreu...@nmr.mgh.harvard.edugt; wrote Yes, if this is in the long, you also need to add the -long …. stuff Martin On Apr 28, 2015, at 12:46 AM, prasser lt;pras...@zoho.comgt; wrote: Thanks for your response, not sure if I've quite got it yet. So, after the surfaces are done and we update/edit the the aseg.mgz with say, recon-all -surfsegedit we need to re-run recon-all -autorecon2-cp -autorecon3 On Thu, 23 Apr 2015 06:45:00 -0700 Bruce Fischl lt;fis...@nmr.mgh.harvard.edugt; wrote I would think autorecon2-cp autorecon3 would be fine, but maybe Martin can comment? On Wed, 22 Apr 2015, prasser wrote: gt; Repost.Thanks. gt; gt; gt; On Mon, 20 Apr 2015 16:35:29 -0700 lt;pras...@zoho.comgt; wrote gt; gt; Thank you again for your reply. gt; gt; For editing aseg.mgz, as mentioned in gt; gt; https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegme gt; ntations gt; gt; it does suggest using -autorecon2-noaseg, but from what I can see this does not gt; update the aparc+aseg.mgz and associated .stats etc is that correct? Doesn't gt; this command (as does -autorecon3) also re-create surfaces that would need to be gt; re-checked and re-edited if needed? gt; gt; Also, I think FS5.1 does not have the -autorecon2-noaseg flag. gt; gt; As an alternative, with completed wm/pial boundaries could we run gt; gt; recon-all -surfsegedit, gt; gt; then we would edit aseg as needed and then: gt; gt; recon-all -aparc2aseg -segstats -wmparc gt; gt; This will not change any surfaces but would update aseg.stats gt; aparc.a2009s+aseg.mgz wmparc.mgz wmparc.stats etc gt; gt; P gt; gt; gt; On Mon, 20 Apr 2015 13:42:49 -0700 Martin gt; Reuterlt;mreu...@nmr.mgh.harvard.edugt; wrote gt; Hi gt; gt; so take a look at gt; https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData gt; where the entry points are described ( for brainmask and finalsurfs gt; -autorecon-pial should be OK, for aseg it says to use gt; gt; -autorecon2-noaseg ) gt; Also this page gt; https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags gt; has details on the steps. gt; gt; Best, Martin gt; gt; gt; gt; On 04/20/2015 03:21 PM, Martin Reuter wrote: gt; gt; usually edits to surfaces should not be required in the long. The gt; surfaces there get initialized from the base, so you need to make gt; sure the base surface is as accurate as possible. Several edits also gt; get transferred automatically from the cross sectional runs. See gt; this gt; http://freesurfer.net/fswiki/LongitudinalEdits gt; for a description of the different edits, and where they should be gt; done. gt; gt; About where to restart after making the edits, everything should be gt; done the same way as in the regular (cross sectional) processing. gt; So you specifically ask about: gt; - brainmask edits gt; - brainfinalsurf edits gt; - and manual aseg edits. gt; gt; I just looked at the description of those regular edits gt; http://freesurfer.net/fswiki/Edits gt; but sadly there it does not say where to start re-run either. I'll gt; try to find out and update that soon. gt; gt; I hope someone with editing experience can chime in and tell us. (I gt; changed the subject, so that it get's read). gt; gt; Cheers, Martin gt; gt; On 04/20/2015 09:44 AM, Bruce Fischl wrote: gt; gt; cheers gt; Bruce gt; gt; gt; On Mon, 20 Apr 2015, prasser wrote: gt; gt; Dear All, gt; I wanted to check that corrections to a Long pial gt; surface through edits gt; to brainmask.mgz and brain.finalsurfs.manedit.mgz gt; are followed by the gt; command: gt; recon-all -long tpN1 templateID -autorecon2-pial gt; -autorecom3 gt; gt; Is this correct? gt; gt; Also, after editing the Long aseg.mgz to correct gt; the volume of structures gt; what command should be run to have these edits gt; update the dependent files? gt; gt; Thanks, gt; gt; P gt; gt; gt; gt; gt; gt; ___ Freesurfer mailing list freesur...@nmr.mgh.h gt; arvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer gt; gt; gt; -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neurosci gt; ence Dept. of Radiology,
Re: [Freesurfer] where to start recon-all after edits
Thanks Martin. The concern I have with using -autorecon2-cp -autorecon3 after -surfsegedit is that, new surfaces are created during -autorecon2-cp -autorecon3 so that aseg and the surfaces are always out of step with each other. Any suggestions on how I could test the validity of the method described here as an alternative: recon-all -surfsegedit then edit aseg if needed and then: recon-all -aparc2aseg -segstats -wmparc On Tue, 05 May 2015 07:09:48 -0700 Martin Reuter lt;mreu...@nmr.mgh.harvard.edugt; wrote Yes, if this is in the long, you also need to add the -long …. stuff Martin On Apr 28, 2015, at 12:46 AM, prasser lt;pras...@zoho.comgt; wrote: Thanks for your response, not sure if I've quite got it yet. So, after the surfaces are done and we update/edit the the aseg.mgz with say, recon-all -surfsegedit we need to re-run recon-all -autorecon2-cp -autorecon3 On Thu, 23 Apr 2015 06:45:00 -0700 Bruce Fischl lt;fis...@nmr.mgh.harvard.edugt; wrote I would think autorecon2-cp autorecon3 would be fine, but maybe Martin can comment? On Wed, 22 Apr 2015, prasser wrote: gt; Repost.Thanks. gt; gt; gt; On Mon, 20 Apr 2015 16:35:29 -0700 lt;pras...@zoho.comgt; wrote gt; gt; Thank you again for your reply. gt; gt; For editing aseg.mgz, as mentioned in gt; gt; https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegme gt; ntations gt; gt; it does suggest using -autorecon2-noaseg, but from what I can see this does not gt; update the aparc+aseg.mgz and associated .stats etc is that correct? Doesn't gt; this command (as does -autorecon3) also re-create surfaces that would need to be gt; re-checked and re-edited if needed? gt; gt; Also, I think FS5.1 does not have the -autorecon2-noaseg flag. gt; gt; As an alternative, with completed wm/pial boundaries could we run gt; gt; recon-all -surfsegedit, gt; gt; then we would edit aseg as needed and then: gt; gt; recon-all -aparc2aseg -segstats -wmparc gt; gt; This will not change any surfaces but would update aseg.stats gt; aparc.a2009s+aseg.mgz wmparc.mgz wmparc.stats etc gt; gt; P gt; gt; gt; On Mon, 20 Apr 2015 13:42:49 -0700 Martin gt; Reuterlt;mreu...@nmr.mgh.harvard.edugt; wrote gt; Hi gt; gt; so take a look at gt; https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData gt; where the entry points are described ( for brainmask and finalsurfs gt; -autorecon-pial should be OK, for aseg it says to use gt; gt; -autorecon2-noaseg ) gt; Also this page gt; https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags gt; has details on the steps. gt; gt; Best, Martin gt; gt; gt; gt; On 04/20/2015 03:21 PM, Martin Reuter wrote: gt; gt; usually edits to surfaces should not be required in the long. The gt; surfaces there get initialized from the base, so you need to make gt; sure the base surface is as accurate as possible. Several edits also gt; get transferred automatically from the cross sectional runs. See gt; this gt; http://freesurfer.net/fswiki/LongitudinalEdits gt; for a description of the different edits, and where they should be gt; done. gt; gt; About where to restart after making the edits, everything should be gt; done the same way as in the regular (cross sectional) processing. gt; So you specifically ask about: gt; - brainmask edits gt; - brainfinalsurf edits gt; - and manual aseg edits. gt; gt; I just looked at the description of those regular edits gt; http://freesurfer.net/fswiki/Edits gt; but sadly there it does not say where to start re-run either. I'll gt; try to find out and update that soon. gt; gt; I hope someone with editing experience can chime in and tell us. (I gt; changed the subject, so that it get's read). gt; gt; Cheers, Martin gt; gt; On 04/20/2015 09:44 AM, Bruce Fischl wrote: gt; gt; cheers gt; Bruce gt; gt; gt; On Mon, 20 Apr 2015, prasser wrote: gt; gt; Dear All, gt; I wanted to check that corrections to a Long pial gt; surface through edits gt; to brainmask.mgz and brain.finalsurfs.manedit.mgz gt; are followed by the gt; command: gt; recon-all -long tpN1 templateID -autorecon2-pial gt; -autorecom3 gt; gt; Is this correct? gt; gt; Also, after editing the Long aseg.mgz to correct gt; the volume of structures gt; what command should be run to have these edits gt; update the dependent files? gt; gt; Thanks, gt; gt; P gt; gt; gt; gt; gt; gt; ___ Freesurfer mailing list freesur...@nmr.mgh.h gt; arvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer gt; gt; gt; -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neurosci gt; ence Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusett gt; s General Hospital Research Affiliate Computer Science and Artificial Intelligence
Re: [Freesurfer] where to start recon-all after edits
Yes, if this is in the long, you also need to add the -long …. stuff Martin On Apr 28, 2015, at 12:46 AM, prasser pras...@zoho.com wrote: Thanks for your response, not sure if I've quite got it yet. So, after the surfaces are done and we update/edit the the aseg.mgz with say, recon-all -surfsegedit we need to re-run recon-all -autorecon2-cp -autorecon3 On Thu, 23 Apr 2015 06:45:00 -0700 Bruce Fischl fis...@nmr.mgh.harvard.edu wrote I would think autorecon2-cp autorecon3 would be fine, but maybe Martin can comment? On Wed, 22 Apr 2015, prasser wrote: Repost.Thanks. On Mon, 20 Apr 2015 16:35:29 -0700 pras...@zoho.com mailto:pras...@zoho.com wrote Thank you again for your reply. For editing aseg.mgz, as mentioned in https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegme https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegme ntations it does suggest using -autorecon2-noaseg, but from what I can see this does not update the aparc+aseg.mgz and associated .stats etc is that correct? Doesn't this command (as does -autorecon3) also re-create surfaces that would need to be re-checked and re-edited if needed? Also, I think FS5.1 does not have the -autorecon2-noaseg flag. As an alternative, with completed wm/pial boundaries could we run recon-all -surfsegedit, then we would edit aseg as needed and then: recon-all -aparc2aseg -segstats -wmparc This will not change any surfaces but would update aseg.stats aparc.a2009s+aseg.mgz wmparc.mgz wmparc.stats etc P On Mon, 20 Apr 2015 13:42:49 -0700 Martin Reutermreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu wrote Hi so take a look at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData where the entry points are described ( for brainmask and finalsurfs -autorecon-pial should be OK, for aseg it says to use -autorecon2-noaseg ) Also this page https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags has details on the steps. Best, Martin On 04/20/2015 03:21 PM, Martin Reuter wrote: usually edits to surfaces should not be required in the long. The surfaces there get initialized from the base, so you need to make sure the base surface is as accurate as possible. Several edits also get transferred automatically from the cross sectional runs. See this http://freesurfer.net/fswiki/LongitudinalEdits http://freesurfer.net/fswiki/LongitudinalEdits for a description of the different edits, and where they should be done. About where to restart after making the edits, everything should be done the same way as in the regular (cross sectional) processing. So you specifically ask about: - brainmask edits - brainfinalsurf edits - and manual aseg edits. I just looked at the description of those regular edits http://freesurfer.net/fswiki/Edits http://freesurfer.net/fswiki/Edits but sadly there it does not say where to start re-run either. I'll try to find out and update that soon. I hope someone with editing experience can chime in and tell us. (I changed the subject, so that it get's read). Cheers, Martin On 04/20/2015 09:44 AM, Bruce Fischl wrote: cheers Bruce On Mon, 20 Apr 2015, prasser wrote: Dear All, I wanted to check that corrections to a Long pial surface through edits to brainmask.mgz and brain.finalsurfs.manedit.mgz are followed by the command: recon-all -long tpN1 templateID -autorecon2-pial -autorecom3 Is this correct? Also, after editing the Long aseg.mgz to correct the volume of structures what command should be run to have these edits update the dependent files? Thanks, P ___ Freesurfer mailing list freesur...@nmr.mgh mailto:freesur...@nmr.mgh.h arvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neurosci ence Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusett s General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technolog y A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu
Re: [Freesurfer] where to start recon-all after edits
I would think autorecon2-cp autorecon3 would be fine, but maybe Martin can comment? On Wed, 22 Apr 2015, prasser wrote: Repost.Thanks. On Mon, 20 Apr 2015 16:35:29 -0700 pras...@zoho.com wrote Thank you again for your reply. For editing aseg.mgz, as mentioned in https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegme ntations it does suggest using -autorecon2-noaseg, but from what I can see this does not update the aparc+aseg.mgz and associated .stats etc is that correct? Doesn't this command (as does -autorecon3) also re-create surfaces that would need to be re-checked and re-edited if needed? Also, I think FS5.1 does not have the -autorecon2-noaseg flag. As an alternative, with completed wm/pial boundaries could we run recon-all -surfsegedit, then we would edit aseg as needed and then: recon-all -aparc2aseg -segstats -wmparc This will not change any surfaces but would update aseg.stats aparc.a2009s+aseg.mgz wmparc.mgz wmparc.stats etc P On Mon, 20 Apr 2015 13:42:49 -0700 Martin Reutermreu...@nmr.mgh.harvard.edu wrote Hi so take a look at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData where the entry points are described ( for brainmask and finalsurfs -autorecon-pial should be OK, for aseg it says to use -autorecon2-noaseg ) Also this page https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags has details on the steps. Best, Martin On 04/20/2015 03:21 PM, Martin Reuter wrote: usually edits to surfaces should not be required in the long. The surfaces there get initialized from the base, so you need to make sure the base surface is as accurate as possible. Several edits also get transferred automatically from the cross sectional runs. See this http://freesurfer.net/fswiki/LongitudinalEdits for a description of the different edits, and where they should be done. About where to restart after making the edits, everything should be done the same way as in the regular (cross sectional) processing. So you specifically ask about: - brainmask edits - brainfinalsurf edits - and manual aseg edits. I just looked at the description of those regular edits http://freesurfer.net/fswiki/Edits but sadly there it does not say where to start re-run either. I'll try to find out and update that soon. I hope someone with editing experience can chime in and tell us. (I changed the subject, so that it get's read). Cheers, Martin On 04/20/2015 09:44 AM, Bruce Fischl wrote: cheers Bruce On Mon, 20 Apr 2015, prasser wrote: Dear All, I wanted to check that corrections to a Long pial surface through edits to brainmask.mgz and brain.finalsurfs.manedit.mgz are followed by the command: recon-all -long tpN1 templateID -autorecon2-pial -autorecom3 Is this correct? Also, after editing the Long aseg.mgz to correct the volume of structures what command should be run to have these edits update the dependent files? Thanks, P ___ Freesurfer mailing list freesur...@nmr.mgh.h arvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neurosci ence Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusett s General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technolog y A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edureu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list freesur...@nmr.mgh.h arvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neurosci ence Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusett s General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technolog y A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edureu...@mit.edu Web : http://reuter.mit.edu
Re: [Freesurfer] where to start recon-all after edits
Repost.Thanks. On Mon, 20 Apr 2015 16:35:29 -0700 lt;pras...@zoho.comgt; wrote Thank you again for your reply. For editing aseg.mgz, as mentioned in https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations it does suggest using -autorecon2-noaseg, but from what I can see this does not update the aparc+aseg.mgz and associated .stats etc is that correct? Doesn't this command (as does -autorecon3) also re-create surfaces that would need to be re-checked and re-edited if needed? Also, I think FS5.1 does not have the -autorecon2-noaseg flag. As an alternative, with completed wm/pial boundaries could we run recon-all -surfsegedit, then we would edit aseg as needed and then: recon-all -aparc2aseg -segstats -wmparc This will not change any surfaces but would update aseg.stats aparc.a2009s+aseg.mgz wmparc.mgz wmparc.stats etc P On Mon, 20 Apr 2015 13:42:49 -0700 Martin Reuterlt;mreu...@nmr.mgh.harvard.edugt; wrote Hi so take a look at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData where the entry points are described ( for brainmask and finalsurfs -autorecon-pial should be OK, for aseg it says to use -autorecon2-noaseg ) Also this page https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags has details on the steps. Best, Martin On 04/20/2015 03:21 PM, Martin Reuter wrote: blockquote cite=mid:lt;agt;553551cf.30...@nmr.mgh.harvard.edu type=cite gt;= hi= p, usually edits to surfaces should not be required in the long. The surfaces there get initialized from the base, so you need to make sure the base surface is as accurate as possible. Several edits also get transferred automatically from the cross sectional runs. See this http://freesurfer.net/fswiki/LongitudinalEdits for a description of the different edits, and where they should be done. About where to restart after making the edits, everything should be done the same way as in the regular (cross sectional) processing. So you specifically ask about: - brainmask edits - brainfinalsurf edits - and manual aseg edits. I just looked at the description of those regular edits http://freesurfer.net/fswiki/Edits but sadly there it does not say where to start re-run either. I'll try to find out and update that soon. I hope someone with editing experience can chime in and tell us. (I changed the subject, so that it get's read). Cheers, Martin On 04/20/2015 09:44 AM, Bruce Fischl wrote: blockquote cite=mid:alpilt;agt;ne.lrh.2.11.1504200944020.9...@gate.nmr.mgh.harvard.edu type=cite gt;i'll= leave= the= first= question= for= martin= but= it= looks= right= to= me= (except= typo= in= what= should= be= -autorecon3).= second= one= i= think= you= want= rerun= mri_segstats= and= mris_anatomical_stats= commands,= which= done= by= autorecon3= cheers Bruce On Mon, 20 Apr 2015, prasser wrote: Dear All, I wanted to check that corrections to a Long pial surface through edits to brainmask.mgz and brain.finalsurfs.manedit.mgz are followed by the command: recon-all -long tpN1 templateID -autorecon2-pial -autorecom3 Is this correct? Also, after editing the Long aseg.mgz to correct the volume of structures what command should be run to have these edits update the dependent files? Thanks, P ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] where to start recon-all after edits
Hi so take a look at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData where the entry points are described ( for brainmask and finalsurfs -autorecon-pial should be OK, for aseg it says to use -autorecon2-noaseg ) Also this page https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags has details on the steps. Best, Martin On 04/20/2015 03:21 PM, Martin Reuter wrote: Hi P, usually edits to surfaces should not be required in the long. The surfaces there get initialized from the base, so you need to make sure the base surface is as accurate as possible. Several edits also get transferred automatically from the cross sectional runs. See this http://freesurfer.net/fswiki/LongitudinalEdits for a description of the different edits, and where they should be done. About where to restart after making the edits, everything should be done the same way as in the regular (cross sectional) processing. So you specifically ask about: - brainmask edits - brainfinalsurf edits - and manual aseg edits. I just looked at the description of those regular edits http://freesurfer.net/fswiki/Edits but sadly there it does not say where to start re-run either. I'll try to find out and update that soon. I hope someone with editing experience can chime in and tell us. (I changed the subject, so that it get's read). Cheers, Martin On 04/20/2015 09:44 AM, Bruce Fischl wrote: I'll leave the first question for Martin but it looks right to me (except for the typo in what should be -autorecon3). For the second one I think you want to rerun the mri_segstats and mris_anatomical_stats commands, which should be done by autorecon3 cheers Bruce On Mon, 20 Apr 2015, prasser wrote: Dear All, I wanted to check that corrections to a Long pial surface through edits to brainmask.mgz and brain.finalsurfs.manedit.mgz are followed by the command: recon-all -long tpN1 templateID -autorecon2-pial -autorecom3 Is this correct? Also, after editing the Long aseg.mgz to correct the volume of structures what command should be run to have these edits update the dependent files? Thanks, P ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web :http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] where to start recon-all after edits
Thank you again for your reply. For editing aseg.mgz, as mentioned in https://surfer.nmr.mgh.harvard.edu/fswiki/TkMeditGuide/TkMeditWorkingWithData/FreeviewSegmentations it does suggest using -autorecon2-noaseg, but from what I can see this does not update the aparc+aseg.mgz and associated .stats etc is that correct? Doesn't this command (as does -autorecon3) also re-create surfaces that would need to be re-checked and re-edited if needed? Also, I think FS5.1 does not have the -autorecon2-noaseg flag. As an alternative, with completed wm/pial boundaries could we run recon-all -surfsegedit, then we would edit aseg as needed and then: recon-all -aparc2aseg -segstats -wmparc This will not change any surfaces but would update aseg.stats aparc.a2009s+aseg.mgz wmparc.mgz wmparc.stats etc P On Mon, 20 Apr 2015 13:42:49 -0700 Martin Reuterlt;mreu...@nmr.mgh.harvard.edugt; wrote Hi so take a look at https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingData where the entry points are described ( for brainmask and finalsurfs -autorecon-pial should be OK, for aseg it says to use -autorecon2-noaseg ) Also this page https://surfer.nmr.mgh.harvard.edu/fswiki/OtherUsefulFlags has details on the steps. Best, Martin On 04/20/2015 03:21 PM, Martin Reuter wrote: 553551cf.30...@nmr.mgh.harvard.edu type=citegt; Hi P, usually edits to surfaces should not be required in the long. The surfaces there get initialized from the base, so you need to make sure the base surface is as accurate as possible. Several edits also get transferred automatically from the cross sectional runs. See this http://freesurfer.net/fswiki/LongitudinalEdits for a description of the different edits, and where they should be done. About where to restart after making the edits, everything should be done the same way as in the regular (cross sectional) processing. So you specifically ask about: - brainmask edits - brainfinalsurf edits - and manual aseg edits. I just looked at the description of those regular edits http://freesurfer.net/fswiki/Edits but sadly there it does not say where to start re-run either. I'll try to find out and update that soon. I hope someone with editing experience can chime in and tell us. (I changed the subject, so that it get's read). Cheers, Martin On 04/20/2015 09:44 AM, Bruce Fischl wrote: ne.lrh.2.11.1504200944020.9...@gate.nmr.mgh.harvard.edu type=citegt;I'll leave the first question for Martin but it looks right to me (except for the typo in what should be -autorecon3). For the second one I think you want to rerun the mri_segstats and mris_anatomical_stats commands, which should be done by autorecon3 cheers Bruce On Mon, 20 Apr 2015, prasser wrote: Dear All, I wanted to check that corrections to a Long pial surface through edits to brainmask.mgz and brain.finalsurfs.manedit.mgz are followed by the command: recon-all -long tpN1 templateID -autorecon2-pial -autorecom3 Is this correct? Also, after editing the Long aseg.mgz to correct the volume of structures what command should be run to have these edits update the dependent files? Thanks, P ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Dr. Martin Reuter Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe
