Hi Reza,

 

Thank you for your fast reply.

 

It was my fault. On the page (http://www.fmrib.ox.co.uk/fsl/randomize/index.html) I have read  that fslmaths can be used to test TFCE „on an existing stats image”. But it seems it is true just after applying randomise. Is it correct? Or what else „fslmaths –tfce” is for?

 

Another questions. According to the page mentioned above „randomise” is an option for simple GLM (t-tests, one-way ANOVA, simple  correlation). In fMRI it means some cases of higher level analysis. What about 2-way ANOVAs? What about 1st level, where design matrix contains canonical HRF? And when we use nuisance effects (e.g. motion-correction parameters, or temporal derivative of HRF), the exchangeability of data is not assured. Does it means that randomise is not advised to use in these cases?

 

Best,

 

Auer, Tibor M.D.

Biomedizinische NMR Forschungs GmbH

am Max-Planck Institut für Biophysikalische Chemie

Am Fassberg 11

37077 Göttingen

Germany

Phone/Work: +49-(0)551-201-1725

Phone/Home: +49-(0)551-250-4576

Mobile: +49-(0)176-8012-7921

Mail: [log in to unmask]

 

From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Reza Salimi
Sent: Monday, March 02, 2009 11:01 AM
To: [log in to unmask]
Subject: Re: [FSL] TFCE in fMRI

 

Hi Tibur,

applying the TFCE to a statistical map (i.e., a t- or  z-stat map) cannot be directly used for a statistical inference (i.e., thresholding to find activation blobs in the brain),

and since there is no parametric form for the TFCE statistic, you need to run a nonparametric (randomise) analysis, with TFCE inference and threshold the output p-value volume (which is  *tfce*corrp* volume in randomise).

cheers

 

 

 

 

2009/3/2 Auer, Tibor MD. <[log in to unmask]>

Dear FSL Users,

I try to use TFCE (Threshold Free Cluster Enhancement) in fMRI. I have read that "fslmath" can apply TFCE on a previously calculated statistical map (e.g. ztats1.nii.gz).

To make everything easier, I have written a script to produce activation map after TFCE (see attached).
I used the pre-fixed options 2 0.5, and according to my understanding thresholded the resulted image with 0.95 to get p=0.05 equivalent. The rest of the script is just to overlay and produce image.

The attached script produces more sensitive however quite noisy image.
I ask someone with more knowledge on TFCE to check whether my implementation is correct.

Thanks,

Auer, Tibor M.D.

Biomedizinische NMR Forschungs GmbH

am Max-Planck Institut für Biophysikalische Chemie

Am Fassberg 11

37077 Göttingen

Germany

Phone/Work: +49-(0)551-201-1725

Phone/Home: +49-(0)551-250-4576

Mobile: +49-(0)176-8012-7921

Mail: [log in to unmask]

 

 




--
G. Salimi-Khorshidi,
D.Phil. Student, Dept. of Clinical Neurology, University of Oxford.
[log in to unmask]    http://www.fmrib.ox.ac.uk/~reza
FMRIB Centre, John Radcliffe Hospital,
Headington, Oxford,  OX3 9DU
Tel: +44 (0) 1865 222466  Fax: +44 (0)1865 222717