Hi Doug Thanks for helping me with this!
First time around I did everything as is outlined in 'Define a Region of Interest' here: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis. I'll try your suggestion now. The input data would be something like ?h.volume.fwhm10.fsaverage.mgh, correct? Thanks again Courtney -----Original Message----- From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Sent: Thursday, March 31, 2011 5:44 PM To: Gallen, Courtney (NIH/NIDA) [F] Cc: Nick Schmansky; Freesurfer Mailing List Subject: Re: [Freesurfer] Interpreting results from Qdec Hi Courtney, did you transfer the label to each individual subject using mri_label2label? A better way to replicate your qdec results is to run mri_segstats on the input data to qdec (y.mgh usually). Specify the label with "--slabel subject hemi yourlabel". Also specify "--avgwf subjectdata.txt". This will create this text file with a list of the input data for each subject averaged over your label. doug Gallen, Courtney (NIH/NIDA) [F] wrote: > Hi Nick > > I'm revisiting this issue and have a few more questions. First, I have a > significant interaction between two variables on cortical volume. I drew a > label on this ROI and ran mris_anatomical_stats on the label (thank you for > that suggestion). > > For stats in the output table file, is the column 'GrayVol' the same thing as > the cortical volume I looked at in Qdec? I'm asking because when I export > GrayVol values into SPSS, there is no longer a significant interaction > between my variables (and if this ROI is significant after multiple > comparisons across the brain, I'd expect the mean volume from the ROI to be > very significant in SPSS). > > Please let me know if my questions aren't clear. Thanks in advance > Courtney > > > Courtney Gallen > Post-baccalaureate IRTA > Neuroimaging Research Branch > National Institute on Drug Abuse (IRP) > 251 Bayview Blvd > Suite 200 > Baltimore, MD 21224 > Tel: (443) 740-2631 > > > -----Original Message----- > From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] > Sent: Thursday, January 13, 2011 3:08 PM > To: Gallen, Courtney (NIH/NIDA) [F] > Cc: Freesurfer Mailing List > Subject: Re: [Freesurfer] Interpreting results from Qdec > > Courtney, > > if i understand your question, i think one way to do that is to use qdec > to draw a label on the blob of interest, and the run 'map label to > subjects', which creates a label file in each subjects label dir, then > you can run stats on that with mris_anatomical_stats. > > (btw, i'm putting this answer on the list, as others may have better > ideas.) > > n. > > > > On Mon, 2011-01-03 at 16:38 -0500, Gallen, Courtney (NIH/NIDA) [F] > wrote: > >> Hi Nick >> >> Thanks for the prompt reply. Sorry if my questions seem a bit naïve--this is >> my first time using Freesurfer. >> >> A follow up question to your answer for question 1. I see that the group >> data will be plotted in Qdec for significant blobs, but say there is a >> significant interaction between two variables and it's not entirely apparent >> what is driving this interaction. >> Is there a way to extract the mean of this blob for each individual (i.e., >> treat it as an ROI or something similar) to determine what's driving the >> significance? >> >> Thanks in advance! >> Courtney >> >> -----Original Message----- >> From: Nick Schmansky [mailto:ni...@nmr.mgh.harvard.edu] >> Sent: Thursday, December 30, 2010 2:44 PM >> To: Gallen, Courtney (NIH/NIDA) [F] >> Cc: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] Interpreting results from Qdec >> >> ans. 1. - the easiest way is to Ctrl- left mouse click on a blob, and a >> plot of the data at that surface vertex will appear. the group will be >> apparent from that (say, demented group is thinner than non-demented >> group). this data is significance data (log p, so '2' is 0.01), so mean >> and stdev wouldnt apply in that case. the file 'y.mgh' is the raw data >> of all subjects in the analysis, so you could extract mean and stdev >> from that. >> >> ans. 2. - slide the 'annotation' opacity slider to show the annotation >> data (cortical parcellation). the ctrl left click will also put the >> region info for that vertex on the lower left of the display. >> >> see also: >> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QdecGroupAnalysis >> >> n. >> >> On Wed, 2010-12-29 at 10:49 -0500, Gallen, Courtney (NIH/NIDA) [F] >> wrote: >> >>> Hi, >>> >>> >>> >>> I’m currently running analyses in Qdec and have identified areas that >>> show significant effects in my contrasts. I have two questions related >>> to interpreting these results. >>> >>> >>> >>> 1. How can you interpret the effect in each “blob?” (i.e., which >>> group has a greater cortical surface area, etc.). Right now, all I >>> know is that there is an effect in certain areas. Can you export this >>> data to get means and standard errors? >>> >>> 2. Is there a way to localize where these effects are? E.g., a >>> tool that tells you this effect is located in __ area of the brain? >>> >>> >>> >>> Thanks in advance >>> >>> Courtney >>> >>> >>> >>> Courtney Gallen >>> >>> Post-baccalaureate IRTA >>> >>> Neuroimaging Research Branch >>> >>> National Institute on Drug Abuse (IRP) >>> >>> 251 Bayview Blvd >>> >>> Suite 200 >>> >>> Baltimore, MD 21224 >>> >>> Tel: (443) 740-2631 >>> >>> >>> _______________________________________________ >>> 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. >> >> >> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
