Hi Anderson, 

So If I have 24 rows of my design1_contrast.con file, and then 24 columns of my ftest file, then the numerator of df is 24, correct? 

ftoz -zout fzstat fstat1 134 24 

Would give me the correctly converted Z statistic for my F-tests? 

Also, you recommended using FEAT instead of the command line.  Did you mean setting it up in the FEAT gui? I haven't been doing that because the FEAT gui freezes when I try to enter this model, because it has so many EVs. I cannot get a work around so that this doesn't happen. If you have any suggests I would greatly appreciate! 

Alternatively, is there a way to hand-make the .fsf file without having to open the GUI to enter my design? Can I use a .fsf file to only perform cluster thresholding on the f-test files?

Thanks!

On Thu, Dec 8, 2016 at 5:33 AM, Anderson M. Winkler <[log in to unmask]> wrote:

Hi Michelle,

F-tests have the same DOF as the t-test (for the denominator). For the numerator, the t test has always df=1 (usually omitted) and the F-test has DOF that is the same as the number of lines in the contrast (e.g., for a simple 3 group comparison with or without nuisance variables, it's 2).

All the best,

Anderson

On 7 December 2016 at 18:31, Michelle VanTieghem <[log in to unmask]> wrote:

Hi Anderson, 

Also, how do I determine the DOF for my F-tests? 

For the z-tests I was using # rows in the design - # of columns (207 - 77 = 134)

However, I'm having trouble thinking about what it should be for Ftests since this is a mixed effects design... 

thanks,

Michelle 

On Wed, Dec 7, 2016 at 8:39 AM, Michelle VanTieghem <[log in to unmask]> wrote:

Hi Anderson, 

Do you mean setting it up in the FEAT gui? I haven't been doing that because the FEAT gui freezes when  I try to enter this model, because it has so many EVs. Is there a way to use an .fsf file without having to open the GUI to enter my design? Can I use a .fsf file to only perform cluster thresholding on the f-test files?

Thanks!

M

On Wed, Dec 7, 2016 at 2:55 AM, Anderson M. Winkler <[log in to unmask]> wrote:

Hi Michelle,

You'd use ftoz to convert to a z-score map. That said, if you'll use the random field theory for inference, it might be much simpler and less error-prone to simply use FEAT. It does everything for you and you don't have to worry about these commands.

All the best,

Anderson

On 6 December 2016 at 21:33, Michelle VanTieghem <[log in to unmask]> wrote:

Hi Anderson,

Ok great thanks. I have run the f-tests. Now I would like to use smoothest and cluster in order to identify significant clusters of activation for F4, the Group x Emotion interaction. However, cluster, as far as I can tell from the information on FSL wiki, is used with zstat files.
Can I do the same exact thing, but replace zstat files (of a specific contrast) with the fstat files (to test the omnibus interaction)?
When testing F-tests in cluster, does make sense to use a t- threshold (e.g. 3.1)?
I would think there should be F threshold, but that doesn't appear to be an option in cluster....
Here is an example of what I would like to do:

smoothest -d 134 -r res4d.nii.gz -m mask.nii.gz >> cluster_correction/smoothness_output_wholebrain_mask.txt

fslmaths fstat4.nii.gz -mas mask.nii.gz cluster_correction/fstat4_mask.nii.gz

cluster -i fstat4_mask.nii.gz -t 3.1 -o fstat4_clusters_3.1 -d 0.043 --volume=234781 -p .05 --othresh=fstat4_thresh_3.1.nii.gz > cluster_info_wholebrain_3.1_fstat4.txt

I appreciate any input!
Thank you,
Michelle

--

Michelle VanTieghem

PhD student in Psychology

Developmental Affective Neuroscience Lab

Columbia University 

[log in to unmask]

--

Michelle VanTieghem

PhD student in Psychology

Developmental Affective Neuroscience Lab

Columbia University 

[log in to unmask]

--

Michelle VanTieghem

PhD student in Psychology

Developmental Affective Neuroscience Lab

Columbia University 

[log in to unmask]