Try using this version of mri_segstats ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats doug
On 03/20/2013 01:10 PM, Laura M. Tully wrote: > the mri_segstats command did not work - below is the command and > output. It looks like it is searching for the .annot file in fsaverage > directory. How do I tell it to use fsaverage and to look for the > .annot elsewhere? > > cd glmdir > > mri_segstats --i beta.mgh --annot fsaverage lh > ./SZcontrast_oneGrp_oneBehVar_4CVs/cache.th13.abs.sig.ocn.annot > --avgwf > lh.SZ_CPT_area_betas.dat --excludeid 0 > > > $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ > > cwd > > cmdline mri_segstats --i beta.mgh --annot fsaverage lh > ./SZcontrast_oneGrp_oneBehVar_4CVs/cache.th13.abs.sig.ocn.annot > --avgwf > lh.SZ_CPT_area_betas.dat --excludeid 0 > > sysname Linux > > hostname ncfws12.rc.fas.harvard.edu > <http://ncfws12.rc.fas.harvard.edu> > > machine x86_64 > > user ltully > > Constructing seg from annotation > > could not read annot file > > /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh../SZcontrast_oneGrp_oneBehVar_4CVs/cache.th13.abs.sig.ocn.annot.annot > > No such file or directory > > > Thanks! > > LT > > On Wed, Mar 20, 2013 at 9:54 AM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > > On 03/20/2013 12:09 PM, Laura M. Tully wrote: > > 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? > > It is an annotation > > > * 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? > > No > > > > * 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 > > That looks correct. Did it work? Add --excludeid 0 to keep it from > reporting on non-clusters > > > > * how does one convert an xxx.ocn.annot file to a label? > > If needed, use mri_annotation2label > > > * 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? > > It is probably easiest if you treat each glm separately. You can > break the annotations into separate labels, then recombine the > labels into another annotation (mris_label2annot), but it is a lot > of work. > > > * > > > * 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? > > Yes. They are in $FREESURFER_HOME/matlab and > $FREESURFER_HOME/fsfast/toolbox > doug > > > * > > > Thanks in advance for your help! > > Laura. > > > On Wed, Mar 20, 2013 at 8:29 AM, 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: > > > 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> > <mailto:tully.la...@googlemail.com > <mailto:tully.la...@googlemail.com>> > <mailto:tully.la...@googlemail.com > <mailto:tully.la...@googlemail.com> > > <mailto: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> <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>> <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/ > > 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> <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> <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 > > > > > -- > -- > 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
