it depends what they are. You can look in the other stats files to see if they are there (we include a couple of cortical parcellations). If they aren't, you can draw them yourself on fsaverage and map them to all your subjects using our spherical transform

cheers Bruce On Fri, 27 May 2016, Marja Caverlé wrote:

Hi Bruce,

Thanks, that indeed includes most of the roi's I want to include. What if there are some area's that are not in that list? Is there a way of adding areas?

Best,

Marja

On Fri, May 27, 2016 at 10:26 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Marja

  what ROI do you mean? We generate lots of them, and tabulate the
  thickness within each one. Look for example in <subject
  id>/stats/aparc.stats

  cheers
  Bruce
  On Fri, 27 May 2016, Marja Caverlé wrote:

        Hi all,

        So I ran a recon-all -all on one of my subjects, and
        it completed without
        errors (according to the log). Now I would like to
        get cortical thickness
        numbers from this subject, but when I open the
        tutorial regarding this, it
        says it assumes that you already have a roi mask and
        a T1 in the same
        coordinate space as the roi mask. 

        Did the recon -all -all by any chance create these
        files? And if not, how
        can I?

        So basically the question is; what do I have to do
        after recon -all -all in
        order to get cortical thickness numbers in roi's of
        my subjects?

        Thanks in advance.

        Marja

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yes, they are based on different atlases. You can look at the original papers (Rahul Desikan's is one and Christophe Destriuex's is the other) to see the differences. Or you can load the various .annot files in freeview on the inflated surface to see them visually

cheers Bruce On Fri, 27 May 2016, Marja Caverlé wrote:

Hi Bruce,

Thanks for the fast response! I indeed found them in other stats files. What is the difference between these files? I assume they are based on different atlases? I saw that there are some slight differences between the numbers in different files for the same structures, so how do I know which file I should use?

Thank you so much for your help!

Best,

Marja

On Fri, May 27, 2016 at 11:00 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: it depends what they are. You can look in the other stats files to see if they are there (we include a couple of cortical parcellations). If they aren't, you can draw them yourself on fsaverage and map them to all your subjects using our spherical transform

  cheers
  Bruce
  On Fri, 27 May 2016, Marja Caverlé wrote:

        Hi Bruce,

        Thanks, that indeed includes most of the roi's I
        want to include. What if
        there are some area's that are not in that list? Is
        there a way of adding
        areas?

        Best,

        Marja

        On Fri, May 27, 2016 at 10:26 PM, Bruce Fischl
        <fischl@nmr.mgh.harvard.edu>
        wrote:
              Hi Marja

              what ROI do you mean? We generate lots of
        them, and tabulate the
              thickness within each one. Look for example in
        <subject
              id>/stats/aparc.stats

              cheers
              Bruce
              On Fri, 27 May 2016, Marja Caverlé wrote:

                    Hi all,

                    So I ran a recon-all -all on one of my
        subjects, and
                    it completed without
                    errors (according to the log). Now I
        would like to
                    get cortical thickness
                    numbers from this subject, but when I
        open the
                    tutorial regarding this, it
                    says it assumes that you already have a
        roi mask and
                    a T1 in the same
                    coordinate space as the roi mask. 

                    Did the recon -all -all by any chance
        create these
                    files? And if not, how
                    can I?

                    So basically the question is; what do I
        have to do
                    after recon -all -all in
                    order to get cortical thickness numbers
        in roi's of
                    my subjects?

                    Thanks in advance.

                    Marja


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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.