yes, something like ?h.volume.fwhm10.fsaverage.mgh doug Gallen, Courtney (NIH/NIDA) [F] wrote: > 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 >> >> >> >> > >
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