Here are two subjects (attached)

On Wed, Oct 30, 2013 at 11:31 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:

Hi Ashley

if you upload a dataset we'll take a look. I am surprised to hear that you are having problems. Can you post an example image?

Bruce

On Wed, 30 Oct 2013, Ashley Hannah wrote:

Hello,

...

Has anyone processed a SAG FSPGR BRAVO sequence successfully through FreeSurfer?

When I run these images the program finishes without error however the output in tksurfer is grossly incorrect.

Is there a way to adjust the parameters for reading white and gray matter by freesurfer (because BRAVO has a different contrast, not as defined) so that regions and boundaries are parceled correctly?

Thanks,

Ashley

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.

It's hard to tell anything from those images. We need to see surfaces over volumes in freeview or tkmedit Cheers Bruce

On Oct 30, 2013, at 12:01 PM, Ashley Hannah ahannah1510@gmail.com wrote:

For some reason the images will not display.

Hopefully this works....

...

On Wed, Oct 30, 2013 at 11:31 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Ashley

if you upload a dataset we'll take a look. I am surprised to hear that you are having problems. Can you post an example image?

Bruce

On Wed, 30 Oct 2013, Ashley Hannah wrote:

...

Hello, Has anyone processed a SAG FSPGR BRAVO sequence successfully through FreeSurfer?

When I run these images the program finishes without error however the output in tksurfer is grossly incorrect.

Is there a way to adjust the parameters for reading white and gray matter by freesurfer (because BRAVO has a different contrast, not as defined) so that regions and boundaries are parceled correctly?

Thanks,

Ashley

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.

-- Ashley M. Hannah Doctoral Student Neuroscience Program Michigan State University <SAGBravo2_07.png> <SAGBravo1_07.png>

looks like a pretty severe bias field may be the source of much of your problems (plus some motion artifact) On Wed, 30 Oct 2013, Ashley Hannah wrote:

Here are the tkmedit with overlay images.

Thank you for your help!

Ashley

On Wed, Oct 30, 2013 at 12:40 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: It's hard to tell anything from those images. We need to see surfaces over volumes in freeview or tkmedit Cheers Bruce

On Oct 30, 2013, at 12:01 PM, Ashley Hannah ahannah1510@gmail.com wrote:

  For some reason the images will not display.

Hopefully this works....

On Wed, Oct 30, 2013 at 11:31 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Ashley

  if you upload a dataset we'll take a look. I am
  surprised to hear that you are having problems. Can
  you post an example image?

  Bruce
  On Wed, 30 Oct 2013, Ashley Hannah wrote:

        Hello, 
        Has anyone processed a SAG FSPGR BRAVO
        sequence successfully through
        FreeSurfer?

        When I run these images the program
        finishes without error however the
        output  in tksurfer is grossly
        incorrect. 

        Is there a way to adjust the parameters
        for reading white and gray matter by
        freesurfer (because BRAVO has a
        different contrast, not as defined) so
        that
        regions and boundaries are parceled
        correctly?

        Thanks, 
        --
        Ashley

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.

-- Ashley

  <SAGBravo2_07.png>

  <SAGBravo1_07.png>

-- Ashley

yes, you can add control points to the white matter if that's what's going on Bruce On Wed, 30 Oct 2013, Ashley Hannah wrote:

Can this be manually corrected?

On Wed, Oct 30, 2013 at 2:19 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: looks like a pretty severe bias field may be the source of much of your problems (plus some motion artifact) On Wed, 30 Oct 2013, Ashley Hannah wrote:

        Here are the tkmedit with overlay images.

        Thank you for your help!

        Ashley



        On Wed, Oct 30, 2013 at 12:40 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              It's hard to tell anything from those images.
        We need to see
              surfaces over volumes in freeview or tkmedit
        Cheers
        Bruce

        On Oct 30, 2013, at 12:01 PM, Ashley Hannah
        <ahannah1510@gmail.com>
        wrote:

              For some reason the images will not display.
        Hopefully this works....


        On Wed, Oct 30, 2013 at 11:31 AM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu> wrote:
              Hi Ashley

              if you upload a dataset we'll take a look. I
        am
              surprised to hear that you are having
        problems. Can
              you post an example image?

              Bruce
              On Wed, 30 Oct 2013, Ashley Hannah wrote:

                    Hello, 
                    Has anyone processed a SAG FSPGR BRAVO
                    sequence successfully through
                    FreeSurfer?

                    When I run these images the program
                    finishes without error however the
                    output  in tksurfer is grossly
                    incorrect. 

                    Is there a way to adjust the parameters
                    for reading white and gray matter by
                    freesurfer (because BRAVO has a
                    different contrast, not as defined) so
                    that
                    regions and boundaries are parceled
                    correctly?

                    Thanks, 
                    --
                    Ashley




        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.




        --
        Ashley

              <SAGBravo2_07.png>

              <SAGBravo1_07.png>




        --
        Ashley

-- Ashley M. Hannah Doctoral Student Neuroscience Program Michigan State University