Hi,
I am trying to run the randomise function on my data. I have 19 subjects who had 2 scans (day1 and day2) and I want to compare diffusion metrics (FA) between days, within-subjects (Single-Group Paired Difference, Paired T-Test). I created a design matrix and contrast matrix following the example here: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/GLM#Single-Group_Paired_Difference_.28Paired_T-Test.29
This is my design matrix:
/NumWaves 20
/NumPoints 38
/Matrix
1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
-1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-1 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-1 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-1 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0
-1 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0
-1 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0
-1 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0
-1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
-1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0
-1 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0
-1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0
-1 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0
-1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0
-1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0
-1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
-1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0
-1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
and this is my contrast matrix:
1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Still following the example from the link above, I computed the difference in FA between day1 and day2 (fslmaths -sub), then merged the difference for all 19 subjects into a 4D file (fslmerge -t d1_minus_d2_fa *d1-d2_FA.nii.gz). This 4D image is my input in the randomise function and it has 19 volumes (4th dimension=19).
randomise(d1_minus_d2_FA, output_rootname_FA, design_mat, contrast_mat, mask_image)
I got the error: "Loading Data: ERROR: Program failednumber of rows in design matrix doesn't match number of "time points" in input data!"
I also tried with a design matrix containing only 19 rows and 1 column (all 1) and a contrast matrix with only 1 value (1) to try to fix this issue. This time, I get a Warning: "tfce has detected a large number of integral steps. This operation may require a great deal of time to complete" and it has been stuck there for a while.
I would really appreciate your help,
Thank you,
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