OK, thanks!
Gabriella
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, January 11, 2016 2:31 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fMRI activation color inversion
no, it is a matter of taste. Note that 2 is the threshold. If you are looking at sig maps, then the threshold may be important. The p-value threshold is 10^-fthresh
On 01/11/2016 02:19 PM, Hirsch, Gabriella wrote:
Thanks Doug! This is very good to know. Is there a ratio or relationship between the fmin and fmax that is optimal, as in, should we keep a 2 to 5 ratio?
Gabriella
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, January 11, 2016 12:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] fMRI activation color inversion
There is another parameter called -fmid. The final mapping is a complicated combination of all three (fthresh, fmin, fslope). I usally use the -fminmax option which is easier to explain. -fminmax 2 5 means that the threshold is set to 2 and that at 5 the color will saturate. doug
On 01/11/2016 12:18 PM, Hirsch, Gabriella wrote:
Hi FreeSurfer experts,
I recently ran a simple fMRI analysis in FSL and now generating images of the activation in freesurfer using reg-feat2anat to register the functional activation to the freesurfer recon-all files, and generating the images using tksurfer:
/tksurfer pilot_3 lh inflated -annot aparc.annot -ov run4578_COMB.gfeat/cope1.feat/stats/zstat1.nii.gz -ovreg run4_fwhm8.feat/reg/freesurfer/anat2std.register.dat *-fthresh 4 *-fslope 1/
However I have come across a strange occurrence when I change the threshold. Specifically, when I set the -fthresh flag (bolded) as 4 (i.e. p=0.0001) or less, the activation colors comes off as they should (see 4_blue attached) in terms of how I set up the contrasts. But when I set my threshold to 5 or higher (changing nothing else), the colors of the activation invert (see 5_red attached).
What does this mean? How can I fix this?
Any ideas would be greatly appreciated!
Thank you! Gabriella
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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