Well, that is bad (beacuse there is a bug) and good (because now it is known) at the same time. I wanted to estimate a p-value for a group of voxels of interest for a certain contrast in my analysis. Instead of averaging the p values for these voxels, I thought it would make more sense to calculate the average t statistic for the voxels and then estimate the p-value for the group of voxels myself using tcdf function in matlab. So, I guess I need the t values for that, unless I can think of a workaround, which so far I couldn't.
Best, Pablo
On Thu, Nov 11, 2010 at 11:57 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu
wrote:
Hi Pablo, you have found a bug in FSFAST in which the values in the t.nii file are actually the sqrt of the p-values. I have fixed it in our code base and it will be in the next version. Do you actually need the t-values?
thanks!
doug
Pablo Polosecki wrote:
I understand the X.mat contains the variable DOF which tells me the degrees of freedom for the analysis, right? In my case it is 5915. This is what I get when I load X.mat into a structure named 'x':
x =
DoSynth: 0 UseFloat: 0 SynthSeed: -1 flac0: [1x1 struct] runflac: [1x21 struct] X: [6048x133 double] DOF: 5915 rfm: [1x1 struct] yrun_randn: []RescaleFactor: 5.6510 ErrCovMtx: 0 acfseg: [1x1 struct] acfsegmn: [6048x1 double] nrho1segmn: 0.1456 W: [6048x6048 double]
On Thu, Nov 11, 2010 at 11:35 AM, Douglas N Greve < greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
what is your dof?
Pablo Polosecki wrote:
Oh, sure. It is: t.vol(test_voxel_number) ans = -0.6368 On Thu, Nov 11, 2010 at 10:25 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: sorry, I meant what is the actual value of the t in t.vol(test_voxel_number)? Pablo Polosecki wrote: Firstly, thank you for the quickyresponse. t.vol is the t-volume, loaded from t.nii using the MRIread function (i.e. t=MRIread('t.nii');). test_voxel_number is just some voxel of the volume that I'm using as an example in this sanity check (I set it to 4000 in the sample code but it could have been anything else). I'm using -(abs(t.vol(test_voxel_number) )) because that is how I think the p-value is calculated from the t-statistic is a 2 tailed test. (See for instance the matlab code of the built-in ttest.m function where you have p = 2 * tcdf(-abs(tval), df) with df being the degrees of freedom.) Still if I used the alternative you sugggest, without the minus sign, I get: my_pval=-log10(2*tcdf((abs(t.vol(test_voxel_number))), x.DOF)) my_pval = -0.1690 While I still have the stored p-value of stored_pval = -0.4055 Thanks again! On Thu, Nov 11, 2010 at 10:02 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: what is t.vol(test_voxel_number)? Why do you use -(abs(t.vol(test_voxel_number))) instead of +(abs(t.vol(test_voxel_number)))? doug Pablo Polosecki wrote: Dear experts, For different reasons I found myself double checking the relationship between t-values in t.nii and p-values stored in sig.nii. If I use the following matlab code I thought that I should get the values of my_pval and stored_pval to be the same (except perhaps for the sign): cd(fullfile(basedir,session,'bold',anal,contrast)) x=load('../X.mat') t=MRIread('t.nii'); sig=MRIread('sig.nii'); test_voxel_number=4000;my_pval=-log10(2*tcdf(-(abs(t.vol(test_voxel_number))), x.DOF)) stored_pval=sig.vol(test_voxel_number)
However I get: stored_pval = -0.4055 my_pval = 0.2804 Am I doing something wrong here? My FreeSurfer version is 4.5 Thank you! -- Pablo Polosecki Graduate Fellow Laboratory of Neural Systems The Rockefeller University 1230 York Avenue, Box 9 New York, NY 10065
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