Hi Anderson,To clarify, group is between subject (not within subject), and emotion is within subject task condition. Therefore, I do think that covariates of age and sex would make a difference. Particularly when I have a very wide age range across a developmental sample. Essentially I would like to do a repeated measures ANCOVA to test for group x Emotion interaction while controlling for individual differences in age, sex, accuracy on the task, ect.. Can you please advise how this can be modeled in the design? I attached my design in the previous email (that generated errors: matrix is singular).Thanks!MichelleOn Tue, Dec 13, 2016 at 4:17 AM, Anderson M. Winkler <[log in to unmask]> wrote:Hi Michelle,So this is a repeated measurements design in which each subject was assessed three times. Since age and sex doesn't change for the 3 visits, these don't need to be modelled, as the subject-specific EVs already take care of these nuisance. So, just remove age and sex from the model.All the best,AndersonOn 12 December 2016 at 23:09, Michelle VanTieghem <[log in to unmask]> wrote:Hi Anderson,Great thanks --that fixed the ftoz conversion error.I would like to include between subject covariates of age and sex in my design1 (group x emotion). However, when I tried to add these covariates into the design matrix, I am getting the following error:An exception has been thrownRuntime error:- detected by Newmat: matrix is singularMatrixType = Crout # Rows = 75; # Cols = 75Trace: Crout(lubksb); GeneralSolv; Gsmanager::flame_stage1_onvoxel; Gsmanager::flame_stage1; Gsmanager::run. I think this means that I did not set up the design properly. See attached for design.mat and contrast file. Can you please advise on how to add covariates to the model, so that I can control for between subject differences in Age and sex?Thanks!MichelleOn Mon, Dec 12, 2016 at 11:13 AM, Anderson M. Winkler <[log in to unmask]> wrote:Hi Michelle,One correction: the dof1 should be the dof of the numerator, so you'd swap the first and second values.All the best,AndersonOn 9 December 2016 at 11:11, Anderson M. Winkler <[log in to unmask]> wrote:Hi Michelle,Yes, the conversion is right. Re: large design, I'm not sure if there is a script that would do it... sorry.All the best,AndersonOn 8 December 2016 at 18:02, Michelle VanTieghem <[log in to unmask]> wrote: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 24Would 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,AndersonOn 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,MichelleOn 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,AndersonOn 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_fs tat4.txt
I appreciate any input!
Thank you,
Michelle
Michelle VanTieghemPhD student in PsychologyDevelopmental Affective Neuroscience LabColumbia University--Michelle VanTieghemPhD student in PsychologyDevelopmental Affective Neuroscience LabColumbia University--Michelle VanTieghemPhD student in PsychologyDevelopmental Affective Neuroscience LabColumbia University--Michelle VanTieghemPhD student in PsychologyDevelopmental Affective Neuroscience LabColumbia University--Michelle VanTieghemPhD student in PsychologyDevelopmental Affective Neuroscience LabColumbia University