Sorry, if you're loading a zstat, then you should interpret the values (and thresholds) as z-stats. doug
On 03/27/2012 04:54 AM, Zurcher Nicole wrote: > Dear Doug, > > Thank you very much for your reply. > > There is one other thing that is not clear to me. When displaying group level > FSL zstats onto the FreeSurfer surface, which threshold (-log10(p) or z > score) should I use? Is it again -log10(p), and therefore p=.01 is 2? > If this is indeed the case, how come that the min and max values that appear > in the min and max of the X axis Range (in the configure overlay display > window) are the actual minimum and maximum values of the z stat map generated > in FSL? This is why I thought that the value used for thresholding the maps > should be a z score value, i.e. for p=0.01, I would have used min=2.3 > (one-tailed). What am I missing? > > Thanks again! > Nicole > > > > On Mar 26, 2012, at 4:23 PM, Douglas N Greve wrote: > >> >> Zurcher Nicole wrote: >>> Hi everyone, >>> I have two questions regarding FreeSurfer and FSL interoperation and it >>> would be great if someone could help. >>> >>> 1) When displaying subject-level FSL FEAT data onto the FS volume using the >>> command "tkmedit blobby orig.mgz lh.white -overlay >>> ./featdir/stats/zstat1.nii.gz -overlay-reg >>> featdir/reg/freesurfer/anat2exf.register.dat fthresh 1.3 -fmid 2.3 -fslope >>> 1” (mentioned on http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html) What >>> /p/-value does the threshold of 1.3 correspond to? Is it a zscore? >> It is -log10(p), so p=.01 is 2 >>> 2) What would be the best way to display FSL group-level FEAT data (zstats) >>> onto the FreeSurfer surface? >>> As far as I understand, the FSL and FreeSurfer Interoperation website >>> explains how to display subject level-feat on the surface. For the >>> group-level data, it only explains how to run group-level analyses using >>> mri_glmfit based on lower-level FSL FEAT directories. Is there a way to >>> directly map the zstats from FSL group-level analyses onto the FreeSurfer >>> surface? >> You can use the $FREESURFER_HOME/average/mni152.register.dat. Note that this >> is for display only. You still have all the shortcomings of doing the >> analysis in the volume. >> doug >>> Thanks in advance for the help! >>> Nicole >>> ------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> 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 >> >> >> >> 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. >> > > -- 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
