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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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

Thank you for your help!

So you are suggesting that after we insert the patch we run "-autorecon2 -autorecon3 -clean-aseg" on all of the subjects who were previously run with the -nocanorm flag? How will this affect the edits previously made on them?

Thank you, Gabe

-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky, MGH Sent: Sunday, October 12, 2014 12:14 PM To: Bruce Fischl Cc: Freesurfer support list Subject: Re: [Freesurfer] v5.1 control point mri_ca_normalize bug

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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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

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