 |
 |
Thank you Anderson, The paper, for which you provided a link, is fascinating, and I should be able to make a similar scatter plot. However, I am conspicuously naive regarding most aspects of FSL; most obviously the shell scripting, and I need to become more familiar with it. Currently, I am uncertain how to extract/compute the effect sizes for each of the 18 subjects in both analysis (tbss_sym and TBSS tests., so a total of 36 effect sizes) . Also, I am uncertain which method would be appropriate to create regions of interest. Nevertheless, I used fslmaths to create roi masks based on the contrast that proved to show a significant between group difference and fslstats to calculate the average effect size. -The TBSS coorp_tstat (here corrp_tstat2) was used to make the TBSS mask fslmaths PD_tbss18_tfce_corrp_tstat2.nii.gz -thr 0.90 -bin tbss_90_th Then fslstats was used fslstats -t full_d_TBSS.nii.gz -k tbss_90_th.nii.gz -M 1.261563 -For tbss_sym fslmaths PD_tbss_sym18_tfce_corrp_tstat2.nii.gz -thr 0.90 -bin tbss_sym_90_th fslstats -t full_d_symLgR.nii.gz -k tbss_sym_90_th.nii.gz -M 1.161762 Again, if this is correct it fails to provide the full range of effect sizes for all 18 subjects in both tests. All the best, Charlie On Sat, Aug 9, 2014 at 2:15 PM, Anderson M. Winkler <[log in to unmask]> wrote: > Hi Charlie, > > Hmm, you'd like to look whether the effect of group differences is larger > or smaller than the effect of latero-lateral differences, is this correct? > I think the graphical representation as in the other email would be the > most informative. Nonetheless, to compute the actual values that summarise > the whole group, these calls aren't correct. The -m in fslmeants is to > define a mask only, and the result you found (about 0.48) is just the > average FA value for the brain, not an effect size. > > I'd instead use fslmaths to compute the effect size (as you are doing), > and then average within some regions of interest using fslstats (but > fslmeants would work too). These regions would be the same regions that > you'd use for the scatter plots. You could then show these average values > in the same plots, to complement them. > > All the best, > > Anderson > > > > On 9 August 2014 00:28, Charles Leger <[log in to unmask]> wrote: > >> Hi Anderson, >> >> I neglected to follow-up on the effect size information for the two >> tests. Here is a short recap. >> >> >> Using the same patient and control groups, FA data was analyzed >> initially using TBSS then subsequently examined using the tbss_sym FA >> script. The design and contrast files were identical, and the number of >> permutations was identical (5000). >> >> At alpha .10 (fslview .90) significant differences occurred in both >> tests, but at alpha .05 there was only a significant between group >> difference in the tbss_sym script results. A cursory comparison of Cohen’d >> results suggests somewhat similar effect sizes for the both tests: >> >> At p <.10 , using peak MNI coordinates from the cluster report to locate >> peak coordinates in each test, the ratio of TBSS (mean=1.9) to tbss_sym FA >> (mean=2.4) effect sizes at these coordinates is about 1.26, and TBSS has >> about a 10% greater effect size. I then tried using fslmaths and fslmeants >> to extract effect size data as follows: >> >> >> For tbss_sym FA >> >> fslmaths raw_tstat1.nii.gz –div 2.12 full_d_sym >> >> fslmeants –i all_FA_symmetrised_skeletonised –m full_d_sym –o >> full_d_sym.txt >> >> >> >> For TBSS >> >> fslmaths raw_tstat1.nii.gz –div 2.12 full_d_TBss >> >> fslmeants –i all_FA_skeletonised.nii.gz –m full_d_TBss –o full_d_TBss.txt >> >> >> Is the usage of fslmaths and fslmeants above is correct? The value 2.12 >> is Cohen’s d for 18 subjects, 2 groups of 9. If the above usage is correct, >> then the mean FA using fslmeants for TBSS is 0.4842 and for tbss_sym >> 0.4881. In other word the effect sizes for both tests are very similar. If >> this is the case, why would tyss_sym have a moderate size cluster (48 >> voxels) survive at .05 while the TBSS analysis showed no significant >> difference between groups at .05? >> >> >> All the best, >> >> Charlie >> >> >> On Wed, Aug 6, 2014 at 6:43 AM, Anderson M. Winkler < >> [log in to unmask]> wrote: >> >>> Hi Charlie, >>> >>> This may be an unduly simplistic interpretation. You need to discuss >>> these results with the principal investigator who is conducting the study, >>> taking into account the structures where the differences appeared, and the >>> role that these may have in whatever training the subjects did. And read >>> what the literature says about the sort of experiment you are doing -- >>> plasticity it seems (?). >>> >>> Regarding which test found more pronounced differences, you may want to >>> use a measure of effect size for this, or maybe show graphically the values >>> for each subject. >>> >>> All the best, >>> >>> Anderson >>> >>> >>> >>> On 5 August 2014 15:20, charlie <[log in to unmask]> wrote: >>> >>>> FSL pundits, >>>> >>>> >>>> Using the same patient and control groups, FA data was analyzed >>>> initially using TBSS then subsequently examined using the tbss_sym FA >>>> script. The design and contrast files were identical, and the number of >>>> permutations was identical (5000). With an alpha level of .90 (0.10) >>>> between group differences (p <0.10, corrected) occurred in both analyses: >>>> in the TBSS results the expert or trained group showed greater left FA than >>>> controls in several structures; the tyss_sym analysis showed leftward FA of >>>> experts in some structures and hence relative rightward FA in the same >>>> structures in controls. >>>> >>>> This suggests that left hemisphere dominance in experts is a >>>> contributing factor of outcomes for both tests, and FA results of the tests >>>> may be correlated. Is this a valid inference? >>>> >>>> At .95 (0.05), only the tbss_sym FA test showed a surviving cluster >>>> (bilateral difference) that differed between the groups. Just considering >>>> the two FA tests, could it be inferred that the tbss_sym FA script is more >>>> sensitive? Or would it be more accurate to say that the bilateral >>>> difference (tbss_sym) is more pronounced than the absolute difference >>>> (TBSS)? >>>> >>>> Any feedback would be much appreciated. Thank you >>>> >>> >>> >> >