Dear all, I run "recon-all -autorecon-pial -s subjects" after editing the pial by PialEdit_tktools. However I only find "-autorecon2-pial" option in recon-all manual. So I donot know whether I should run the "recon-all -s subjects -autorecon3" to complete all the 31 stages? Thanks. All the best.
2013-12-10
Rujing Zha School of Life Science University of Science and Technology of China E-mail: zharj@mail.ustc.edu.cn charujing@gmail.com charujing123@163.com
Dear all, Can I just type "recon-all -autorecon-pial -autorecon3 -s subjects" after editing the pial by PialEdit_tktools? All the best
2013-12-10
Rujing Zha School of Life Science University of Science and Technology of China E-mail: zharj@mail.ustc.edu.cn charujing@gmail.com charujing123@163.com
发件人："Rujing Zha" zharj@mail.ustc.edu.cn 发送时间：2013-12-10 12:03 主题：[Freesurfer] after PialEdit_tktools 收件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄送：
Dear all, I run "recon-all -autorecon-pial -s subjects" after editing the pial by PialEdit_tktools. However I only find "-autorecon2-pial" option in recon-all manual. So I donot know whether I should run the "recon-all -s subjects -autorecon3" to complete all the 31 stages? Thanks. All the best.
2013-12-10
Rujing Zha School of Life Science University of Science and Technology of China E-mail: zharj@mail.ustc.edu.cn charujing@gmail.com charujing123@163.com
yes, with "-s subjects" replaced with "-s <subject id>"
On Tue, 10 Dec 2013, Rujing Zha wrote:
Dear all, Can I just type "recon-all -autorecon-pial -autorecon3 -s subjects" after editing the pial by PialEdit_tktools? All the best 2013-12-10
Rujing Zha School of Life Science
University of Science and Technology of China
E-mail:
zharj@mail.ustc.edu.cn
charujing@gmail.com
charujing123@163.com
发件人："Rujing Zha" zharj@mail.ustc.edu.cn 发送时间：2013-12-10 12:03 主题：[Freesurfer] after PialEdit_tktools 收件人："freesurfer"freesurfer@nmr.mgh.harvard.edu 抄送： Dear all, I run "recon-all -autorecon-pial -s subjects" after editing the pial by PialEdit_tktools. However I only find "-autorecon2-pial" option in recon-all manual. So I donot know whether I should run the "recon-all -s subjects -autorecon3" to complete all the 31 stages? Thanks. All the best. 2013-12-10
Rujing Zha School of Life Science
University of Science and Technology of China
E-mail:
zharj@mail.ustc.edu.cn
charujing@gmail.com
charujing123@163.com
Hi Rujing,
yes, you should run -autorecon2-pial -autorecon3
cheers Bruce On Tue, 10 Dec 2013, Rujing Zha wrote:
Dear all, I run "recon-all -autorecon-pial -s subjects" after editing the pial by PialEdit_tktools. However I only find "-autorecon2-pial" option in recon-all manual. So I donot know whether I should run the "recon-all -s subjects -autorecon3" to complete all the 31 stages? Thanks. All the best. 2013-12-10
Rujing Zha School of Life Science
University of Science and Technology of China
E-mail:
zharj@mail.ustc.edu.cn
charujing@gmail.com
charujing123@163.com
Dear Bruce, In PialEdit_tktools http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_tktools, it say this: recon-all -autorecon-pial -subjid pial_edits_before .So I didnot know whether the "-autorecon-pial" option "-autorecon2-pial" option I can run. Would you please tell me which one I should use? Thanks. All the best.
2013-12-10
Rujing Zha
发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu 发送时间：2013-12-10 21:17 主题：Re: [Freesurfer] after PialEdit_tktools 收件人："Rujing Zha"zharj@mail.ustc.edu.cn 抄送："freesurfer"freesurfer@nmr.mgh.harvard.edu
Hi Rujing,
yes, you should run -autorecon2-pial -autorecon3
cheers Bruce On Tue, 10 Dec 2013, Rujing Zha wrote:
Dear all, I run "recon-all -autorecon-pial -s subjects" after editing the pial by PialEdit_tktools. However I only find "-autorecon2-pial" option in recon-all manual. So I donot know whether I should run the "recon-all -s subjects -autorecon3" to complete all the 31 stages? Thanks. All the best.
2013-12-10
Rujing Zha School of Life Science
University of Science and Technology of China
E-mail:
zharj@mail.ustc.edu.cn
charujing@gmail.com
charujing123@163.com
_______________________________________________ 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.
sorry, looking at the script, I think:
recon-all -autorecon-pial -s <subject name>
should be all you need, but perhaps someone else can confirm.
Bruce
On Tue, 10 Dec 2013, Rujing Zha wrote:
Dear Bruce, In PialEdit_tktools http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_tktools, it say this:
recon-all -autorecon-pial -subjid pial_edits_before .So I didnot know whether the "-autorecon-pial" option "-autorecon2-pial" option I can run. Would you please tell me which one I should use? Thanks. All the best. 2013-12-10
Rujing Zha
发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu 发送时间：2013-12-10 21:17 主题：Re: [Freesurfer] after PialEdit_tktools 收件人："Rujing Zha"zharj@mail.ustc.edu.cn 抄送："freesurfer"freesurfer@nmr.mgh.harvard.edu Hi Rujing, yes, you should run -autorecon2-pial -autorecon3 cheers Bruce On Tue, 10 Dec 2013, Rujing Zha wrote:
Dear all, I run "recon-all -autorecon-pial -s subjects" after editing the pial by PialEdit_tktools. However I only find "-autorecon2-pial" option in recon-
all
manual. So I donot know whether I should run the "recon-all -s subjects -autorecon3" to complete all the 31 stages? Thanks. All the best. 2013-12-10 _________________________________________________________________________
___
Rujing Zha School of Life Science University of Science and Technology of China E-mail: zharj@mail.ustc.edu.cn charujing@gmail.com charujing123@163.com
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer%C2%A0 The information in this e-mail is intended only for the person to whom it i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline%C2%A0.%C2%A0If%C2%A0the%C2%A0e-mail%C... rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail.
Dear Bruce, Thanks. I see. All the best.
2013-12-10
Rujing Zha
发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu 发送时间：2013-12-10 21:29 主题：Re: [Freesurfer] after PialEdit_tktools 收件人："Rujing Zha"charujing123@163.com 抄送："freesurfer"freesurfer@nmr.mgh.harvard.edu
sorry, looking at the script, I think:
recon-all -autorecon-pial -s <subject name>
should be all you need, but perhaps someone else can confirm.
Bruce
On Tue, 10 Dec 2013, Rujing Zha wrote:
Dear Bruce, In PialEdit_tktools http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_tktools, it say this:
recon-all -autorecon-pial -subjid pial_edits_before .So I didnot know whether the "-autorecon-pial" option "-autorecon2-pial" option I can run. Would you please tell me which one I should use? Thanks. All the best.
2013-12-10
Rujing Zha
发件人：Bruce Fischl fischl@nmr.mgh.harvard.edu 发送时间：2013-12-10 21:17 主题：Re: [Freesurfer] after PialEdit_tktools 收件人："Rujing Zha"zharj@mail.ustc.edu.cn 抄送："freesurfer"freesurfer@nmr.mgh.harvard.edu
Hi Rujing,
yes, you should run -autorecon2-pial -autorecon3
cheers Bruce On Tue, 10 Dec 2013, Rujing Zha wrote:
Dear all, I run "recon-all -autorecon-pial -s subjects" after editing the pial by PialEdit_tktools. However I only find "-autorecon2-pial" option in recon-
all
manual. So I donot know whether I should run the "recon-all -s subjects -autorecon3" to complete all the 31 stages? Thanks. All the best.
2013-12-10
Rujing Zha School of Life Science
University of Science and Technology of China
E-mail:
zharj@mail.ustc.edu.cn
charujing@gmail.com
charujing123@163.com
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 i s addressed. If you believe this e-mail was sent to you in error and the e-ma il contains patient information, please contact the Partners Compliance HelpLi ne at http://www.partners.org/complianceline . If the e-mail was sent to you in e rror but does not contain patient information, please contact the sender and pro perly dispose of the e-mail.
freesurfer@nmr.mgh.harvard.edu
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Rujing Zha