correct (the thing to do is comment-out the addition of the control points).
n. On Wed, 2014-10-08 at 17:05 -0400, Bruce Fischl wrote: > I don't think you want to run with -nocanorm. Just commenting out the > addition of the -f $ControlPointsFile should be sufficient. Right Nick? > On > Wed, 8 Oct 2014, Marx, Gabe wrote: > > > Hi Bruce, > > > > I appreciate the response! > > > > I am sorry, I am a bit confused. The release notes state: > > > > "An option is to disable the running of mri_ca_normalize when re-running > > the -autorecon2 or -autorecon2-cp stage after adding control points by > > adding the flag -nocanorm to the end of recon-all. We will continue to > > investigate a more automated solution to detection of this problem. The > > more permanent workaround for v5.1 users is to edit their recon-all script > > making the following change, which will disable usage of control points > > with ca_norm: > > > > # find these lines: > > set cmd = (mri_ca_normalize) > > if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile) > > > > # and comment-out the second line like this: > > set cmd = (mri_ca_normalize) > > #if($UseControlPoints) set cmd = ($cmd -f $ControlPointsFile) > > > > # then re-run your subjects with the flags: -autorecon2 -autorecon3 > > -clean-aseg" > > > > Are you saying the -nocanorm flag will result in inaccurate data? > > > > Thanks! > > Gabe > > > > -----Original Message----- > > From: freesurfer-boun...@nmr.mgh.harvard.edu > > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl > > Sent: Wednesday, October 08, 2014 8:12 AM > > To: Freesurfer support list > > Subject: Re: [Freesurfer] v5.1 control point mri_ca_normalize bug > > > > Hi Gabe > > > > this wasn't really a bug per-se, just induced some behavior that people > > didn't like. You can't skip the mri_ca_normalize step or the aseg won't be > > accurate. The aseg patch I believe just starts autorecon2-cp after the aseg > > hs been created, but Nick or Zeke can correct me if I'm wrong. > > > > cheers > > Bruce > > > > > > > > On Mon, 6 Oct 2014, Marx, Gabe wrote: > > > >> > >> Hello Freesurfer experts, > >> > >> > >> > >> I had a question regarding the v5.1 control point mri_ca_normalize > >> bug. I read the release notes and know that this bug can be worked > >> around by adding the –nocanorm flag to my recon-all however I have > >> become worried about the ramifications of skipping mri_ca_normalize in my > >> pipeline. > >> Would someone be able to give me a better description as to what > >> mri_ca_normalize is doing and what I am sacrificing by taking it out > >> of my pipeline? Furthermore, in regards to the patch for the recon-all > >> script to fix this bug, what is the patch doing exactly? If I had > >> some data in which I used the –nocanorm flag and other data in which I > >> used the patch would I still be able to make valid analysis if I merged > >> them? > >> Would there be significant inconsistencies? > >> > >> > >> > >> Thanks! > >> > >> > >> > >> Best, > >> > >> Gabe > >> > >> > >> > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > _______________________________________________ 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.
