Dear list, There is an issue that I have been concerned about since the beginning of my FS learning, as I have found somehow contradictory information in the tutorials. Is there a way to do an only recon-all after all the edits have been made to a subject? For example, if you have edited all the possible steps (skullstrip, control points, wm and pial surface) is it possible to use all the flags for each step in one only step? Something like: recon-all -autorecon2-cp -autorecon2-wm -autorecon-pial -autorecon3 -subjid <subject>
Or on the other hand each step needs its own recon-all with its appropriate flag? Thank you
Hi Manuel
-autorecon2-cp runs all the steps that autorecon2-wm does so it is redundant. If you run autorecon2-cp and autorecon3 you will get everything (unless you edit the aseg)
cheers Bruce On Thu, 30 Mar 2017, Manuel Delgado wrote:
Dear list, There is an issue that I have been concerned about since the beginning of my FS learning, as I have found somehow contradictory information in the tutorials. Is there a way to do an only recon-all after all the edits have been made to a subject? For example, if you have edited all the possible steps (skullstrip, control points, wm and pial surface) is it possible to use all the flags for each step in one only step? Something like: recon-all -autorecon2-cp -autorecon2-wm -autorecon-pial -autorecon3 -subjid
<subject>
Or on the other hand each step needs its own recon-all with its appropriate flag? Thank you
-- Manuel Delgado Alvarado, MD Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN
Thank you Bruce. However, doing the recon-all for both the wm and the cp will have the same result as adding the control points and recon-all in a first step, and then doing the wm edits and recon-all again? I think that if you perform the wm edits in the result of having added the cp, the edits you need may be different than if you have not done the cp step previously. Is this right? Thus, even though it is possible to do an only recon-all step for both edits, is it recommendable to do it? On 30/03/17 15:51, Bruce Fischl wrote:
Hi Manuel
-autorecon2-cp runs all the steps that autorecon2-wm does so it is redundant. If you run autorecon2-cp and autorecon3 you will get everything (unless you edit the aseg)
cheers Bruce On Thu, 30 Mar 2017, Manuel Delgado wrote:
Dear list, There is an issue that I have been concerned about since the beginning of my FS learning, as I have found somehow contradictory information in the tutorials. Is there a way to do an only recon-all after all the edits have been made to a subject? For example, if you have edited all the possible steps (skullstrip, control points, wm and pial surface) is it possible to use all the flags for each step in one only step? Something like: recon-all -autorecon2-cp -autorecon2-wm -autorecon-pial -autorecon3 -subjid <subject>
Or on the other hand each step needs its own recon-all with its appropriate flag? Thank you
-- Manuel Delgado Alvarado, MD Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN
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Hi Manuel
yes, that is true. The control points might make the wm edits unnecessary cheers Bruce On Fri, 31 Mar 2017, Manuel Delgado wrote:
Thank you Bruce. However, doing the recon-all for both the wm and the cp will have the same result as adding the control points and recon-all in a first step, and then doing the wm edits and recon-all again? I think that if you perform the wm edits in the result of having added the cp, the edits you need may be different than if you have not done the cp step previously. Is this right? Thus, even though it is possible to do an only recon-all step for both edits, is it recommendable to do it?
On 30/03/17 15:51, Bruce Fischl wrote:
Hi Manuel
-autorecon2-cp runs all the steps that autorecon2-wm does so it is redundant. If you run autorecon2-cp and autorecon3 you will get everything (unless you edit the aseg)
cheers Bruce On Thu, 30 Mar 2017, Manuel Delgado wrote:
Dear list, There is an issue that I have been concerned about since the beginning of my FS learning, as I have found somehow contradictory information in the tutorials. Is there a way to do an only recon-all after all the edits have been made to a subject? For example, if you have edited all the possible steps (skullstrip, control points, wm and pial surface) is it possible to use all the flags for each step in one only step? Something like: recon-all -autorecon2-cp -autorecon2-wm -autorecon-pial -autorecon3 -subjid
<subject>
Or on the other hand each step needs its own recon-all with its appropriate flag? Thank you
-- Manuel Delgado Alvarado, MD Neurology Department Neuroimaging Unit Valdecilla Biomedical Research Institute, IDIVAL Santander, SPAIN
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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly dispose of the e-mail.
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