Re: [Freesurfer] Edits to longitudinal pial surface and aseg
Hi, editing the long does not really introduce much bias I think. It is usually not necessary and it is not recommended, because often it problems in the long are caused by earlier problems in the base or even cross, so it is best to fix it there. Your case seems to be different (problems first occur in long). I would try in one case if editing the long works in your situation. It sounds like it should. Best, Martin On 04/22/2015 08:14 PM, prasser wrote: Repost. Thanks. On Mon, 20 Apr 2015 16:21:38 -0700 *pras...@zoho.com* wrote Thank you for your reply. Yes, I'm finding that it is only small edits that are required in the Long for the case of pial surface errors. It is usually in areas where no editing was required in the cross and base, but the pial surface in the Long extends to include dura or cerebellum. I was hoping just to edit the Long brainmask.mgz and brain.finalsurfs.manedit.mgz and re-run with the command recon-all -long tpN1 templateID -autorecon2-pial -autorecon3 and then re-check the surfaces. The alternative as I see it would be 1. Identify the corresponding locations in the Base (even though it is not a problem in the Base) 2. edit, re-run and re-check the Base 3. delete, create and check all new Longs This second option would take a considerable amount of time and may not solve the problem in one iteration. I'm guessing the concerns with the first method are introducing bias any other concerns with editing the Long? P On Mon, 20 Apr 2015 12:21:51 -0700 *Martin Reuter mreu...@nmr.mgh.harvard.edu mailto:mreu...@nmr.mgh.harvard.edu* 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: 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 listfreesur...@nmr.mgh.harvard.edu mailto: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 mailto:mreu...@nmr.mgh.harvard.edu reu...@mit.edu mailto:reu...@mit.edu Web :http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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
Re: [Freesurfer] Edits to longitudinal pial surface and aseg
Repost.Thanks. On Mon, 20 Apr 2015 16:21:38 -0700 lt;pras...@zoho.comgt; wrote Thank you for your reply. Yes, I'm finding that it is only small edits that are required in the Long for the case of pial surface errors. It is usually in areas where no editing was required in the cross and base, but the pial surface in the Long extends to include dura or cerebellum. I was hoping just to edit the Long brainmask.mgz and brain.finalsurfs.manedit.mgz and re-run with the command recon-all -long tpN1 templateID -autorecon2-pial -autorecon3 and then re-check the surfaces. The alternative as I see it would be 1. Identify the corresponding locations in the Base (even though it is not a problem in the Base) 2. edit, re-run and re-check the Base 3. delete, create and check all new Longs This second option would take a considerable amount of time and may not solve the problem in one iteration. I'm guessing the concerns with the first method are introducing bias any other concerns with editing the Long? P On Mon, 20 Apr 2015 12:21:51 -0700 Martin Reuter lt;mreu...@nmr.mgh.harvard.edugt; 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: 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 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. ___ 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] Edits to longitudinal pial surface and aseg
Thank you for your reply. Yes, I'm finding that it is only small edits that are required in the Long for the case of pial surface errors. It is usually in areas where no editing was required in the cross and base, but the pial surface in the Long extends to include dura or cerebellum. I was hoping just to edit the Long brainmask.mgz and brain.finalsurfs.manedit.mgz and re-run with the command recon-all -long tpN1 templateID -autorecon2-pial -autorecon3 and then re-check the surfaces. The alternative as I see it would be 1. Identify the corresponding locations in the Base (even though it is not a problem in the Base) 2. edit, re-run and re-check the Base 3. delete, create and check all new Longs This second option would take a considerable amount of time and may not solve the problem in one iteration. I'm guessing the concerns with the first method are introducing bias any other concerns with editing the Long? P On Mon, 20 Apr 2015 12:21:51 -0700 Martin Reuter lt;mreu...@nmr.mgh.harvard.edugt; 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: 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 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. ___ 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.
[Freesurfer] Edits to longitudinal pial surface and aseg
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 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.
