Thank you!
On Thu, Mar 21, 2013 at 10:56 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu > wrote: > Yes, the average thickness over the cluster for each subject. > doug > > On 03/21/2013 01:54 PM, Laura M. Tully wrote: > >> Thanks - one last clarification: just to confirm - the values of >> thickness.ocn.y.dat (i.e. analyses with thickness as input) are avg >> thickness over the whole cluster for each subject? If not, how would I get >> the avg thickness value for that cluster for each subject? >> >> LT >> >> >> On Thu, Mar 21, 2013 at 10:49 AM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>>> >> wrote: >> >> >> 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<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<gr...@nmr.mgh.harvard.edu> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu <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 <gr...@nmr.mgh.harvard.edu>> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>> >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>> >> >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu <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**>>> >> <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 >> <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**>>> >> <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 >> <mailto:ltu...@fas.harvard.edu**>>>> >> > 310-267-0170 <tel:310-267-0170> >> <tel:310-267-0170 <tel:310-267-0170>> <tel: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/<http://theclinicalbrain.blogspot.com/> >> > Follow me on Twitter: @tully_laura >> > >> > >> > ______________________________**_________________ >> > Freesurfer mailing list >> > Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >>> >> >> > >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<gr...@nmr.mgh.harvard.edu> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>>> >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu>> >> >> >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> >>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> <tel: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>> <tel: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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/** >> BugReporting <http://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<http://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> >> > >> <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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> >>> >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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**>> >> <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/<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<gr...@nmr.mgh.harvard.edu> >> > >> <mailto:gr...@nmr.mgh.harvard.**edu <gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.**edu <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<http://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<http://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/ <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**> >> <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/<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<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> >> >> <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<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> Outgoing: >> >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<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/ <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<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/ <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 ltu...@fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura
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