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.
- 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
- 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
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