Dear Paul,
1) You find pretty thoroughful info on expert options file here: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertPreferences
2) recon-all -autorecon2-cp -autorecon3 is ok (btw -autorecon2-cp and -autorecon2-wm runs the same commands, at least in version 6.0).
3) There is in the souce code following comment on -T option in mri_fill: min # of neighbors which must be on to retain a point Default value is 1.
Regards,
Antonin
Hello Freesurfer, I have couple questions. 1) If I have 2 commands (e.g., mri_normalize -a 30 and mris_inflate -n 30) and I want recon-all to execute both commands. Should I create 2 different expert opts files or 1 expert opts file with both commands in it? Also, how do I include the expert flag with recon? 2) If I have added control points and wm edits to a subject, it is accurate to start from control points? i.e., recon-all -autorecon2-cp -autorecon3 3) Lastly, I am playing around with mri_fill command and I did like to know what -T flag does? Thank you Best, Paul
Thanks Antonin. For 3) what does " min #of neighbors which must be on to retain a point/specify fill_holes threshold" mean exactly? Also, I noticed a difference in FS v5.3 and FS v6.0 ReconAllTable for creating white matter surface. For v5.3, ?h.white is created as one of the outputs for mris_make_surfaces while for v6.0 it has been replace with ?h.white.preparc. At what stage is the final ?h.white surface created for v6.0? Best, Paul
On Tue, Feb 28, 2017 at 5:05 PM, Antonin Skoch ansk@ikem.cz wrote:
Dear Paul,
- You find pretty thoroughful info on expert options file here:
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertPreferences
- recon-all -autorecon2-cp -autorecon3 is ok (btw -autorecon2-cp and
-autorecon2-wm runs the same commands, at least in version 6.0).
- There is in the souce code following comment on -T option in mri_fill:
min # of neighbors which must be on to retain a point Default value is 1.
Regards,
Antonin
Hello Freesurfer, I have couple questions.
- If I have 2 commands (e.g., mri_normalize -a 30 and mris_inflate -n 30)
and I want recon-all to execute both commands. Should I create 2 different expert opts files or 1 expert opts file with both commands in it? Also, how do I include the expert flag with recon? 2) If I have added control points and wm edits to a subject, it is accurate to start from control points? i.e., recon-all -autorecon2-cp -autorecon3 3) Lastly, I am playing around with mri_fill command and I did like to know what -T flag does? Thank you Best, Paul
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.
Not sure about #3, but the final white surface is created by the second call to mris_make_surfaces. That binary is called twice, the first time it creates the preaparc file
On 03/01/2017 09:41 AM, miracle ozzoude wrote:
Thanks Antonin. For 3) what does " min #of neighbors which must be on to retain a point/specify fill_holes threshold" mean exactly? Also, I noticed a difference in FS v5.3 and FS v6.0 ReconAllTable for creating white matter surface. For v5.3, ?h.white is created as one of the outputs for mris_make_surfaces while for v6.0 it has been replace with ?h.white.preparc. At what stage is the final ?h.white surface created for v6.0? Best, Paul
On Tue, Feb 28, 2017 at 5:05 PM, Antonin Skoch <ansk@ikem.cz mailto:ansk@ikem.cz> wrote:
Dear Paul, 1) You find pretty thoroughful info on expert options file here: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertPreferences <https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertPreferences> 2) recon-all -autorecon2-cp -autorecon3 is ok (btw -autorecon2-cp and -autorecon2-wm runs the same commands, at least in version 6.0). 3) There is in the souce code following comment on -T option in mri_fill: min # of neighbors which must be on to retain a point Default value is 1. Regards, Antonin Hello Freesurfer, I have couple questions. 1) If I have 2 commands (e.g., mri_normalize -a 30 and mris_inflate -n 30) and I want recon-all to execute both commands. Should I create 2 different expert opts files or 1 expert opts file with both commands in it? Also, how do I include the expert flag with recon? 2) If I have added control points and wm edits to a subject, it is accurate to start from control points? i.e., recon-all -autorecon2-cp -autorecon3 3) Lastly, I am playing around with mri_fill command and I did like to know what -T flag does? Thank you Best, Paul _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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
Thanks doug. I know the -T flag in mri_fill means min #of neighbors which must be on to retain a point/specify fill_holes threshold. What does it simply do if I use it in mri_fill? Best, Paul
Sent from my BlackBerry 10 smartphone. Original Message From: Douglas N Greve Sent: Wednesday, March 1, 2017 11:36 AM To: freesurfer@nmr.mgh.harvard.edu Reply To: Freesurfer support list Subject: Re: [Freesurfer] multiple expert options files/ wm and control points
Not sure about #3, but the final white surface is created by the second call to mris_make_surfaces. That binary is called twice, the first time it creates the preaparc file
On 03/01/2017 09:41 AM, miracle ozzoude wrote:
Thanks Antonin. For 3) what does " min #of neighbors which must be on to retain a point/specify fill_holes threshold" mean exactly? Also, I noticed a difference in FS v5.3 and FS v6.0 ReconAllTable for creating white matter surface. For v5.3, ?h.white is created as one of the outputs for mris_make_surfaces while for v6.0 it has been replace with ?h.white.preparc. At what stage is the final ?h.white surface created for v6.0? Best, Paul
On Tue, Feb 28, 2017 at 5:05 PM, Antonin Skoch <ansk@ikem.cz mailto:ansk@ikem.cz> wrote:
Dear Paul,
- You find pretty thoroughful info on expert options file here:
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertPreferences https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertPreferences
- recon-all -autorecon2-cp -autorecon3 is ok (btw -autorecon2-cp
and -autorecon2-wm runs the same commands, at least in version 6.0).
- There is in the souce code following comment on -T option in
mri_fill: min # of neighbors which must be on to retain a point Default value is 1.
Regards,
Antonin
Hello Freesurfer, I have couple questions.
- If I have 2 commands (e.g., mri_normalize -a 30 and mris_inflate -n 30)
and I want recon-all to execute both commands. Should I create 2 different expert opts files or 1 expert opts file with both commands in it? Also, how do I include the expert flag with recon? 2) If I have added control points and wm edits to a subject, it is accurate to start from control points? i.e., recon-all -autorecon2-cp -autorecon3 3) Lastly, I am playing around with mri_fill command and I did like to know what -T flag does? Thank you Best, Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 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
freesurfer@nmr.mgh.harvard.edu
-
Antonin Skoch -
Douglas N Greve -
miracle ozzoude -
miracooloz＠gmail.com