yes the input is area - so to clarify, in order to get the average area for each subject in that cluster I would multiply each subject's values in the xxx.ocn.y.dat file by the number of vertices in the cluster (denoted as NVtxs in the cluster summary?) e.g. 0.761374 * 998 = 759.85mmsq? 

Does the same hold for the y values in a thickness analysis, i.e. when thickness is the input, does each value in the xxx.ocn.y.dat file (e.g. 2.54) represent the average thickness of each vertex and so I must multiply that by the number of vertices to get the average thickness for each subject for that cluster? 

I'm using 5.1.0 - I have no idea if I have the patch for area and volume analyses because I run all my analyses remotely on the harvard imaging server (ncf) - how would I know? And what are the bugs in area/volume analyses in 5.1.0(how could I detect them)?

LT


On Thu, Mar 21, 2013 at 10:02 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:
Hi Laura, I assume the input is area? Then this will compute the average area of each vertex. The area of a vertex is the average area of the triangles around it. To get total area, you can multiple the number that you get from xxx.ocn.y.dat by the number of vertices in the cluster.

doug

ps. What version of FS are you using? If not 5.2, do you have the patch to fix the area and volume analysis?



On 03/21/2013 12:52 PM, Laura M. Tully wrote:
hi Doug,
A follow up question:  when I look at the xxx.ocn.y.dat for a cluster where group differences in surface area have been identified the values are all less than 1 (e.g. 0.761374) even though the cluster size is reported as 680 mmsq. does the y value correspond to .76 mmsq average area for that subject in that cluster or does the y value in the context of surface area analyses represent something else? (or does it need to be multiplied by some factor?)

Thanks!


On Wed, Mar 20, 2013 at 2:39 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote:

    They are the input (mri_glmfit --y y.mgh) averaged over the clusters.
    They are raw input, no detrending.
    doug
    On 03/20/2013 05:16 PM, Laura M. Tully wrote:
    > Hello experts,
    >
    > could someone clarify for me what the y values in the xxx.ocn.y.dat
    > files represent following glmfit-sim? are they the residualized y
    > values of avg cortical thickness in that specific cluster after
    > regressing out the effect of any predictor variables in the glm?
    >
    > Thanks!
    >
    > Laura.
    > --
    > --
    > Laura M. Tully, MA
    > Social Neuroscience & Psychopathology, Harvard University
    > Center for the Assessment and Prevention of Prodromal States, UCLA
    > Semel Institute of Neuroscience
    > ltully@mednet.ucla.edu <mailto:ltully@mednet.ucla.edu>
    <mailto:ltully@mednet.ucla.edu <mailto:ltully@mednet.ucla.edu>>
    > ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu>
    <mailto:ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu>>
    > 310-267-0170 <tel:310-267-0170>

    > --
    > My musings as a young clinical scientist:
    > http://theclinicalbrain.blogspot.com/
    > Follow me on Twitter: @tully_laura
    >
    >
    > _______________________________________________
    > Freesurfer mailing list
    > Freesurfer@nmr.mgh.harvard.edu
    <mailto:Freesurfer@nmr.mgh.harvard.edu>

    > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

    --
    Douglas N. Greve, Ph.D.
    MGH-NMR Center
    greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
    Phone Number: 617-724-2358 <tel:617-724-2358>
    Fax: 617-726-7422 <tel:617-726-7422>

    Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
    <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
    FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
    <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>

    Outgoing:
    ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

    _______________________________________________
    Freesurfer mailing list
    Freesurfer@nmr.mgh.harvard.edu <mailto: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.




--
--
Laura M. Tully, MA
Social Neuroscience & Psychopathology, Harvard University
Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience
ltully@mednet.ucla.edu <mailto:ltully@mednet.ucla.edu>
ltully@fas.harvard.edu <mailto:ltully@fas.harvard.edu>
310-267-0170
--
My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/
Follow me on Twitter: @tully_laura

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/




--
--
Laura M. Tully, MA
Social Neuroscience & Psychopathology, Harvard University
Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience
ltully@mednet.ucla.edu 
ltully@fas.harvard.edu
310-267-0170
--
My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/
Follow me on Twitter: @tully_laura