Sorry - meant to respond to list. Thanks for the response Doug - I have a few follow up questions I hope you can clarify:
> > - is the xxx.ocn.annot file created by mri_glmfit-sim considered a > "label" by freesurfer? or does it need to be converted to a label before I > can use mri_segstats to extract the betas from the cluster(s) in the > xxx.ocn.annot? I tried using the following command line to attempt to > extract the betas from the cluster annotation file created by > mri_glmfit-sim, but received an error: > > mri_segstats --i beta.mgh --annot fsaverage hemi contrast/xxx.ocn.annot > --avgwf avgwf.dat > > > - how does one convert an xxx.ocn.annot file to a label? > > > - If I have run 3 different glms looking at the relationship between > thickness and 3 different behavioral variables, and found 1 (or more) > cluster in each glm using mri_glmfit-sim can I create 1 annotation/label > with all the clusters from the separate glms and then extract the betas > from that one annotation using mri_segstats? Or do I need to treat each glm > separately? > > > - I saw on the listserv some references to matlab functions that > can calculate r square and partial correlations for glms with more than one > predictor variable (e.g pcc between thickness and behavioral variable 1; > pcc between thickness and behavioral variable2; Rsq for overall model) but > I could not find the .m scripts for the functions (MRIread > or fast_glm_pcc?) - would these functions be appropriate and if so where > might I find them? > > Thanks in advance for your help! > > Laura. > > > On Wed, Mar 20, 2013 at 8:29 AM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> >> On 03/20/2013 10:17 AM, Laura M. Tully wrote: >> > Hi, >> > >> > I wanted to re-post my questions from a couple of days ago below, but >> > with some more specific questions following a search through the >> > archives. >> > >> > I want to be able to extract the beta values from a cluster identified >> > using mc-z in a group by behavioral variable interaction so that I can >> > 1) plot the relationship of thickness to behavioral variable data by >> > group in that cluster, 2) conduct post hoc tests to examine the >> > interaction, and 3) calculate the Rsquare and partial correlations for >> > each variable in the glm (i.e. how much variation in thickness is >> > explained by my behavioral variable). >> > >> > To extract the beta values from a cluster identified by mc-z would I >> > treat the cluster like a label and use mri_segstats to extract the >> > beta weights from the cluster? Would I need to make a label of all the >> > clusters that I want to do this for first? >> You can do it label by label. Or, if the annotation created by >> mri_glmfit-sim has all the clusters you want, you can use that (also in >> mri_segstats). You can also create an annotation from individual labels >> with mris_label2annot. >> > >> > Is there a way to calculate the basic statistics for the glm and >> > extract in table form? i.e. Fs and ps for peaks of each cluster? What >> > about Rsquare, or the correlation between thickness and my behavioral >> > variable in the clusters? or would I need to compute these outside of >> > freesurfer using the extracted betas? >> You will need to do it outside of FS. What are Fs and ps? >> doug >> >> > >> > Thank you! >> > >> > Laura. >> > >> > >> > >> > >> > >> > >> > On Mon, Mar 18, 2013 at 5:05 PM, Laura M. Tully >> > <tully.la...@googlemail.com <mailto:tully.la...@googlemail.com>> wrote: >> > >> > Hi Freesurfer experts, >> > >> > I'm hoping you can help me understand how to interpret >> > interactions in clusters identified in whole brain analysis using >> > glmfit and glmfit-sim. Below I describe what I've done and what >> > I'd like to be able to do. Any suggestions would be most >> appreciated! >> > >> > * I have two groups (patients, controls) and a behavioral >> > variable of interest (social functioning). I am interested in >> > cortical thickness differences between groups (main effect of >> > group), whether cortical thickness relate to social >> > functioning across the group (main effect of social >> > functioning), and whether this relationship differs by group >> > (group x social functioning interaction). >> > * I ran whole brain analysis using mri_glmfit with group and >> > functioning as variables of interest whilst controlling >> > for/regressing out gender, age, and mean thickness. i.e. 4 >> > classes (conmale,confemale, ptmale, ptfemale) and 3 continuous >> > variables (age, AvgThickness, Functioning) = 16 regressors. >> > * I tested the group x functioning interaction with the >> > following contrast - is it correct? >> > >> > 0000000000000.50.5-0.5-0.5 >> > >> > * I then ran mri_glmfit-sim to identify clusters that survive >> > multiple comparisons. This revealed 4 clusters (3 in LH; 1 in >> > RH) that represent regions showing significant group x >> > functioning interaction. >> > * I visualized the clusters in tksurfer, and by loading the >> > y.fsgd file was able to visualize the plotted data to get a >> > sense of the interaction, but this is as much as I know in >> > terms of how to examine interactions in the cluster data...... >> > >> > My specifc questions include: >> > >> > * I understand that the values in xxx.sig.cluster.mgh overlay >> > reflect log10 p values, the signs of which indicate the >> > direction of the relationship (i.e. -3 = negative correlation >> > between thickness & variable) but I'm not sure how to >> > interpret this in the context of an interaction with group? >> > * I understand that the values in xxx.y.ocn.dat contain the >> > average thickness value for each subject in that cluster and >> > that in a simple between groups test this data could be used >> > to conduct post hoc t-tests to show the direction of the >> > difference, but again I'm not sure how to use this data in the >> > context of the interaction. What do the values represent in a >> > group x variable interaction? >> > >> > Ideally, I'd like to extract the contrast estimates for each >> > subject in the group x functioning contrast and plot it in another >> > program and conduct pairwise comparisons (t-tests) in order to get >> > a better understanding of the interaction). I'm not sure how to do >> > this - is it possible? My thinking is that I do something similar >> > in fMRI analysis in spm where I can plot the contrasts in a >> > significant cluster and then extract both the average contrast >> > estimates for each group and the contrast estimates for each >> > individual subject. >> > >> > Thanks in advance! >> > >> > 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 <tel:310-267-0170> >> > -- >> > My musings as a young clinical scientist: >> > http://theclinicalbrain.blogspot.com/ >> > Follow me on Twitter: @tully_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 > -- -- 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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