Thanks Bruce, but I'm sure I ran autorecon2-cp autorecon3:

recon-all -autorecon2-cp -autorecon3 -subjid.

However, is it ok to use aseg values post editing even if they look different from the pre editing ones?

Thanks a lot.

Claudia

2013/7/24 Bruce Fischl fischl@nmr.mgh.harvard.edu

Hi Claudia

if you run autorecon2 you will rerun the aseg, which will use the control points to change the subcortical intensity normalization. If you don't want that to happen, you need to run -autorecon2-cp

cheers Bruce

On Wed, 24 Jul 2013, Claudia Dacquino wrote:

Dear Freesurfers,we recently processed a sample of adult patients and

...

then we reran autorecon-2 and

autorecon-3 after editing contol points, white matter and pial surface. We exported the asegstat table both pre and post editing, and we got different volumes for most of the subjects. How is that possible, given that the kind of editing we performed is not supposed to affect subcortical segmentation? Thanks a lot. Claudia

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/**compliancelinehttp://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.

Hi Bruce, I run FS 5.1. So for 5.1 version is it normal that post editing aseg values ar different from pre editing even using autorecon2-cp? Thanks again Claudia

2013/7/24 Bruce Fischl fischl@nmr.mgh.harvard.edu

I think it is, but I would visually inspect them. What FS version are you running? Earlier versions reran the aseg for autorecon2-cp, but 5.3 does not

n Wed, 24 Jul 2013, Claudia Dacquino wrote:

Thanks Bruce,but I'm sure I ran autorecon2-cp autorecon3:

...

recon-all -autorecon2-cp -autorecon3 -subjid.

However, is it ok to use aseg values post editing even if they look different from the pre editing ones?

Thanks a lot.

Claudia

2013/7/24 Bruce Fischl fischl@nmr.mgh.harvard.edu Hi Claudia

  if you run autorecon2 you will rerun the aseg, which will use the

control points to change the subcortical intensity normalization. If you don't want that to happen, you need to run -autorecon2-cp

  cheers
  Bruce


  On Wed, 24 Jul 2013, Claudia Dacquino wrote:

        Dear Freesurfers,we recently processed a sample of adult

patients and then we reran autorecon-2 and autorecon-3 after editing contol points, white matter and pial surface. We exported the asegstat table both pre and post editing, and we got different volumes for most of the subjects. How is that possible, given that the kind of editing we performed is not supposed to affect subcortical segmentation? Thanks a lot. Claudia

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/**compliancelinehttp://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.

I don't think it will change the PV, but I'm not sure

On 07/24/2013 03:40 PM, Bruce Fischl wrote:

I don't think so, but perhaps Nick can comment. Are you positive you didn't run -autorecon2? Actually, maybe the placement of the ribbon will change the partial volume estimates for some subcortical structures? I can't remember the current sequence of events. Nick or Doug: do you know?

On Wed, 24 Jul 2013, Claudia Dacquino wrote:

...

Hi Bruce,I run FS 5.1. So for 5.1 version is it normal that post editing aseg values ar different from pre editing even using autorecon2-cp? Thanks again Claudia

2013/7/24 Bruce Fischl fischl@nmr.mgh.harvard.edu I think it is, but I would visually inspect them. What FS version are you running? Earlier versions reran the aseg for autorecon2-cp, but 5.3 does not n Wed, 24 Jul 2013, Claudia Dacquino wrote:

  Thanks Bruce,but I'm sure I ran autorecon2-cp autorecon3:

  recon-all -autorecon2-cp -autorecon3 -subjid.

  However, is it ok to use aseg values post editing even if
  they look different from the pre editing
  ones?

  Thanks a lot.

  Claudia



  2013/7/24 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
        Hi Claudia

        if you run autorecon2 you will rerun the aseg, which
  will use the control points to change
        the subcortical intensity normalization. If you
  don't want that to happen, you need to run
        -autorecon2-cp

        cheers
        Bruce


        On Wed, 24 Jul 2013, Claudia Dacquino wrote:

              Dear Freesurfers,we recently processed a
  sample of adult patients and then we
              reran autorecon-2 and
              autorecon-3 after editing contol points, white
  matter and pial surface.
              We exported the asegstat table both pre and
  post editing, and we got different
              volumes for most of the
              subjects.
              How is that possible, given that the kind of
  editing we performed is not
              supposed to affect subcortical
              segmentation?
              Thanks a lot.
              Claudia




  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.

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