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Hi Eduardo, Thank you very much for guiding me. All subjects are matched for age, education and will use, tbss and roi analysis for each tracts to get p values. Thanks, Archana # Hi Archana # # It seems the differences is highly distributed across the white matter # tracts. This is fine and a very interesting results indeed. Just make sure # you included all needed covariates in the design model. If this is the # result even after FWE correction, then great. I’m usually very suspicious # of my data when I get such big differences in white matter, but it # happens. # # I see what you want to do, the problem is that you got a big cluster and # it will not show any cut-off point. # The way Anderson says is actually a good way to do it, to run the t-tests # for each ROI. # # What you could also do, and I’m not sure how correct is this, is to use # each tract as a mask (you can get the masks the white matter atlas), # binarize them, and use them to extract the t-values and p-values using # fslmaths. The problem is, each tract will have only one big cluster, but # then you would already have the anatomical location. # # Perhaps someone else has another opinion. # # Hope this helps # # Kind regards # # Eduardo # # #> On Mar 16, 2015, at 3:19 AM, Archana Malagi <[log in to unmask]> wrote: #> #> Hi Eduardo, #> #> Yes, i ran tbss_fill. I want to study white matter differences in two #> language groups using dti metrics. For group comparison, i used two #> sample #> t-test with 10,000 permutations using randomise. #> #> How can i use cluster command with white matter mask? #> #> Thanks, #> Archana #> #> #> #> # Hi Archana #> # #> # The map looks odd to me. Too many areas significant. Did you inflate #> the #> # results using fill? Can you elaborate on the study and the design? #> # #> # Another thing you can do is to extract the p and t values from the #> # clusters #> # using the white matter masks for each white matter tract. #> # #> # Eduardo #> # #> # El Sunday, March 15, 2015, Archana Malagi <[log in to unmask]> #> escribió: #> # #> #> ---------------------------- Original Message #> #> ---------------------------- #> #> Subject: Re: [FSL] How to extract cluster size and p values #> #> From: [log in to unmask] <javascript:;> #> #> Date: Mon, March 16, 2015 10:31 am #> #> To: [log in to unmask] <javascript:;> #> #> #> -------------------------------------------------------------------------- #> #> #> #> Hi Rosalia and Eduardo, #> #> #> #> As discussed, i applied threshold 0.96 , 0.97 while using cluster #> #> command #> #> and also attached snapshot of tbss results : #> #> #> #> threshold 0.96 #> #> #> #> Cluster Index Voxels MAX MAX X (vox) MAX Y (vox) MAX Z #> #> (vox) COG X #> #> (vox) COG Y (vox) COG Z (vox) #> #> 1 32483 0.999 70 150 105 84.3 126 94.2 #> #> #> #> and threshold 0.97 #> #> #> #> Cluster Index Voxels MAX MAX X (vox) MAX Y (vox) MAX Z #> #> (vox) COG X #> #> (vox) COG Y (vox) COG Z (vox) #> #> 1 31264 0.999 70 150 105 84.1 126 94.2 #> #> #> #> #> #> Results of atlasquery with threshold: 0.96 and 0.97 gives same #> results. #> #> #> #> #> #> As a result, it gives only one cluster for both the thresholds and #> most #> #> of #> #> cluster the lies is in right hemisphere. #> #> #> #> Thank you, #> #> #> #> Archana #> #> #> # #> # #> # -- #> # Eduardo A. Garza Villarreal, M.D., Ph.D. #> # #> # #> # - Investigador, *Subdirección de Investigaciones ClÃnicas, #> Instituto #> # Nacional de PsiquiatrÃa.* #> # - Catedrático, *Consejo Nacional de Ciencia y TecnologÃa #> (CONACYT).* #> # - Investigador Asociado, *Center of Functionally Integrative #> # Neuroscience, Universidad de Aarhus, Dinamarca.* #> # - *Profesor-Investigador, Servicio de NeurologÃa, UANL.* #> # - #> # *Coordinador, Unidad de Neurociencias, Centro de Investigación y #> # Desarrollo #> # en Ciencias de la Salud, UANL. * #> # # #