Dear Experts,
I have a very similar case with Romain (I have two timepoint measurements for each subject and I'm interested in the difference between these two timepoints). The GLM experimental design for one-group paired t test on the website is a little different with what Romain made. The Group column in Romain's design is "1 2 3 ..... 1 2 3 ....." while on the website is "1 1 1 .... 1 1 1 ....". Will this kind of design make a difference for the following randomise test?
And just want to make sure I understand correctly, as long as the experimental design matrix are set up like this, and the design.grp to randomise with -e is included, I can directly use the "all_FA_skeletonised.nii.gz" generated by TBSS as the input of randomise. I don't need to manually subtract measurements for each subjest such as
"fslmaths subject1_rA -sub subject1_rB sub1_diff
fslmaths subject2_rA -sub subject2_rB sub2_diff
(repeat for subjects 3-8)
fslmerge -t runA_minus_runB sub1_diff sub2_diff sub3_diff sub4_diff sub5_diff sub6_diff sub7_diff sub8_diff"
The reference webpage link: http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/GLM#Single-Group_Paired_Difference_.28Paired_T-Test.29
I hope I make my question clear.
Thanks for your help.
Best,
Yuchuan
==============The following is the email of Romain's design and Anderson's reply =========================
Hi Romain,
This design is fine as long as you supplied the design.grp file to randomise with the option -e. There's no need to run again doing subtractions, as it'd be equivalent to what was already done.
All the best,
Anderson
2015-01-21 14:09 GMT+00:00 Romain Quentin <[log in to unmask]>:
Dear experts,
I'm analysing FA images with TBSS. I have two scan per participants (run1 and run2).
I did a single-group paired difference with a design.mat like that.
Group EV1 EV2 EV3 EV4 EV5 ....
1 1 1 0 0 0
2 1 0 1 0 0
3 1 0 0 1 0
. . . . . .
. . . . . .
1 -1 1 0 0 0
2 -1 0 1 0 0
3 -1 0 0 1 0
. . . . . .
. . . . . .
On the Glm wiki, you advice to make the substraction manually with fslmaths and run one-sample Ttest.
May I split my all_FA-skeletonised.nii.gz with all images (s1run1, S2run1..., s1run2, s2run2) and substract s1run1 with s1run2, s2run1 with s2run2, ... etc.
Or it is better to re-start from original FA images?
I hope to be clear. Thanks a lot for your help.
Best,
Romain