Dear Anderson,

Thank you for the clarification!

I just finished the TBSS runs and here are the results plus one more question.

In *_tfce_corrp_fstat1.nii.gz i.e FWE corrected f-test result I get two cluster C1 and C2 where 1-p > 0.95

Now on doing individual pariwise t-test I get *_tfce_corrp_tstat3.nii.gz " (B >C) comparison after FWE correction I get the same C1 and C2 cluster where 1-p > 0.95

Similarily for *_tfce_corrp_tstat5.nii.gz " (A >C) comparison after FWE I get the same C1 and C2 cluster where 1-p > 0.95.

Now ever when I look *_tfce_corrp_tstat1.nii.gz " (A >B) comparison after FWE I get a different cluster C3 cluster 1-p> 0.95 but not C1 and C2. C3 is in a anatomically different region than C1 and C2 with no overlap!

I have also saved all the uncorrected-p stats map for each f and t-tests.

Now my question is what is the best way to represent this result. Would my result be based on tfce_corrp_fstats (corrected group f-test) or tfce_corrp_tstats (for corrected individual pairwise t- test)?

Which clusters do I report in my results?

Sorry for bugging you so much on this but deadline is looming over my head!

Kind regards

sourajit

On Fri, Jan 13, 2017 at 4:49 AM, Anderson M. Winkler <[log in to unmask]> wrote:

Hi Sourajit,

Even though there are 3 groups, for the F-test only 2 pairwise comparisons are needed (e.g., A>B and B>C, or A>B and A>C). The reason is that once the test "knows" the difference between A and B, and it also knows the difference between B and C, it automatically knows the difference between A and C. These two pairwise can be in any direction, and don't have to have the signs matching, as the logic remains regardless.

Further, the F-test is two-tailed, so using positive or negative (or any combination thereof) will lead to the same result.

All the best,

Anderson

On 12 January 2017 at 15:04, sourajit mitra <[log in to unmask]> wrote:
Dear Anderson,
Thank you very much for your comments.

However I have one point to clarify.

My groups A, B and C and basically subjects cohorts belonging to 3 stages of the disease.

In such a way that say diffusion parameter FA (A>B>C) progressive decrease

while parameters like Dr (A<B<C) progressive increase.

In such a case wouldn't it be better to have a design.fts like

/NumWaves 6
/NumContrasts 2
/Matrix
1 0 0 1 1 0 i.e F-test between 1st (A>B) , 4th (B>C) and 5th (A>C) t-tests
0 1 1 0 0 1 i.e F-test between 2nd (A<B) , 3rd (B<C) and 6th (A<C) t-tests

rather than having

/NumWaves 6
/NumContrasts 1
/Matrix
1 0 1 0 0 0 F-test between 1st (A>B) and 3rd (B<C) t-tests.

This is off-course with reference to my previous design.con file

EV1(A) EV2(B) EV3(C) CV1 CV2
1 -1 0 0 0 (A>B)
-1 1 0 0 0 (A<B)
0 -1 1 0 0(B<C)
0 1 -1 0 0(B>C)
1 0 -1 0 0(A>C)
-1 0 1 0 0(A<C)

It would be very helpful if you could give your feedback which design.fts should I use?

Kind regards
sourajit

On Thu, Jan 12, 2017 at 5:01 AM, Anderson M. Winkler <[log in to unmask]> wrote:
Ho Sourajit,

Please see below:

On 11 January 2017 at 16:01, Sourajit Mitra Mustafi <[log in to unmask]> wrote:
Dear FSL users,
I have three groups A, B and C; there are also two co variants (CV1 and CV2). At first step I did pairwise t-test between the groups in TBSS runs by using this contrast file

design.con

EV1(A) EV2(B) EV3(C) CV1 CV2
1 -1 0 0 0
-1 1 0 0 0
0 -1 1 0 0
0 1 -1 0 0
1 0 -1 0 0
-1 0 1 0 0

Now I want to perform F-test followed by pairwise t-test.

How do I construct my fts file like "design.fts" and contrast file like "design.con" to achieve this ????

The design.fts would contain:

/NumWaves 6
/NumContrasts 1
/Matrix
1 0 1 0 0 0

This would indicate that the first and third t-tests would constitute the F-test.

Which statistical procedure is more robust just doing individual t-test as I did eariler or doing F-test followed by pairwise t-test?

For only 3 groups it's ok to do the F-test, then the paired t-tests. If more than 2, use the option -corrcon in PALM.

Hope this helps!

All the best,

Anderson

It would be nice if I could get some feedback on this issue