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.
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 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
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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.eduwrote:
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 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
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-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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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
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.**edugreve@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/<http://theclinicalbrain.blogspot.com/> > Follow me on Twitter: @tully_laura > > > ______________________________**_________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<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> <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/> ______________________________**_________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.**harvard.edu Freesurfer@nmr.mgh.harvard.edu>
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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/ 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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/**facility/filedrop/index.htmlhttp://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/
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 <greve@nmr.mgh.harvard.edu mailto: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> <mailto: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>> <mailto: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>> <mailto: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> <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 greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@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 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 -- 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/--
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
freesurfer@nmr.mgh.harvard.edu
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Laura M. Tully