On 03/21/2013 01:11 PM, Laura M. Tully wrote: > 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? Yes, correct > > 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? No, you probably just want to report the average thickness, not the sum of the thicknesses within the 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)? You will need a new version of mris_preproc which you can get from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mris_preproc You can compare this version against the one you have. If they are different, then copy this version into $FREESURFER_HOME/bin. If you are using QDEC, then rerun qcache (recon-all -qcache ...). If you are using the command-line stream, re-run it starting at mris_preproc.
doug > > LT > > > On Thu, Mar 21, 2013 at 10:02 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@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 > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@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 > > ltu...@mednet.ucla.edu <mailto:ltu...@mednet.ucla.edu> > <mailto:ltu...@mednet.ucla.edu <mailto:ltu...@mednet.ucla.edu>> > <mailto:ltu...@mednet.ucla.edu > <mailto:ltu...@mednet.ucla.edu> <mailto:ltu...@mednet.ucla.edu > <mailto:ltu...@mednet.ucla.edu>>> > > ltu...@fas.harvard.edu <mailto:ltu...@fas.harvard.edu> > <mailto:ltu...@fas.harvard.edu <mailto:ltu...@fas.harvard.edu>> > <mailto:ltu...@fas.harvard.edu > <mailto:ltu...@fas.harvard.edu> <mailto:ltu...@fas.harvard.edu > <mailto:ltu...@fas.harvard.edu>>> > > 310-267-0170 <tel:310-267-0170> <tel: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> > <mailto: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 > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto:gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://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> > <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> > <mailto: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 > ltu...@mednet.ucla.edu <mailto:ltu...@mednet.ucla.edu> > <mailto:ltu...@mednet.ucla.edu <mailto:ltu...@mednet.ucla.edu>> > ltu...@fas.harvard.edu <mailto:ltu...@fas.harvard.edu> > <mailto:ltu...@fas.harvard.edu <mailto:ltu...@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 > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@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/ > > > > > -- > -- > Laura M. Tully, MA > Social Neuroscience & Psychopathology, Harvard University > Center for the Assessment and Prevention of Prodromal States, UCLA > Semel Institute of Neuroscience > ltu...@mednet.ucla.edu <mailto:ltu...@mednet.ucla.edu> > ltu...@fas.harvard.edu <mailto:ltu...@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 gr...@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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
