Re: [Freesurfer] y values from glmfit-sim
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.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 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 ___ Freesurfer mailing list 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 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 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 ltu...@fas.harvard.edu 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 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.
Re: [Freesurfer] y values from glmfit-sim
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 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 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 ___ 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 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/ ___ 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 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
Re: [Freesurfer] y values from glmfit-sim
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 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.**edugr...@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** 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 __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.**harvard.eduFreesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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.**edugr...@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/BugReportinghttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting http://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 http://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/ __**_ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:freesur...@nmr.mgh.** harvard.edu Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurferhttps://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
Re: [Freesurfer] y values from glmfit-sim
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
Re: [Freesurfer] y values from glmfit-sim
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.**edugr...@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_preprocftp://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.**edugr...@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.**edugr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edu gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.**edugr...@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
[Freesurfer] y values from glmfit-sim
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 ltu...@fas.harvard.edu 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 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.
