Dr. Smith, Thank you so much for your quick replay and your explanations. Best Regards, Angelica On Thu, 12 Mar 2009 10:23:37 +0000, Steve Smith <[log in to unmask]> wrote: >Hi, > >On 12 Mar 2009, at 02:19, Angelica Hotiu wrote: > >> Dear FSL experts, >> >> I was running TBSS analysis using DTI data acquired from 5 control >> subjects >> and 3 subjects with mild traumatic brain injuries. All the >> preprocessing has >> been done using FSL4.1.2 .I am interested to identify the regions >> where FA, >> MD and transversal diffusivity indicate differences between two >> groups. For >> randomisation procedure I used first TFCE option .As a result FWE >> corrected >> shows the results only for MD. I couldn't obtain FWE corrected for >> multiple >> comparisson for FA and transversal diffusivity using TFCE option. >> Also I >> was trying randomisation using cluster-based thresholding corrected >> for >> multiple comparisons setting different values for threshold but I >> couldn't >> obtain corrected values for p maps in a range [0.95,1]. Based on the >> hypothesis that regions such as corpus callosum, anterior and >> posterior >> limb of internal capsule are more vulnerable to traumatic brain >> injuries I >> was interested to testing this hypothesis for spleninum of corpus >> callosum. >> 1)I'm wondering if this is legal, to limitate TBSS analysis to some >> specific >> region in the brain. > >yes - as long as you honestly had the hypothesis before looking at the >initial randomise results! >Just reduce the mask used in randomise to the region you care about, >as you've done below. > >> 2)If it is, could you please check if it's correct >> draw a mask of spleniunm of corpus callosum (mask_SCC) >> fslmaths mask_SCC -mas mean_FA_skeleton_mask >> mask_SCC_new >> randomise -i all_FA_skeletonised -o tbss -m >> mask_SCC_new -d >> design.mat -t design.con -n 500 - -T2 -V >> As a result of permutation, corrected p image tbss_tfce_corrp_tstat1 >> with >> values [0.95 1] indicate a reduction of FA in mild traumatic brain >> injury >> group in spleninum of corpus callosum. > >Jolly good. > >> 3)I'm wondering about the validity of the previous steps. >> If this is valid, why this result didn't come up by using the >> mean_FA_skeleton_mask as the mask to feed into randomise. > >Because you had more voxels in the mask so the multiple comparison >correction is more aggressive. > >> 4)Another concern is related to the new version v2.1 for randomise. >> I did >> the same analysis for the same subjects using FSL4.1.1 randomise v >> 2.0 and I >> was able to have more results . What is the explanation? Which one >> is more >> recommended? > >That depends on the model - but we've improved the handling of (e.g.) >confound covariates and the interaction between EVs and contrasts wrt >permutation - so the latest approach is more accurate, you should >definitely use the latest version. > >Cheers. > > >> I'm so sorry for the basic questions. Any suggestions will be greatly >> appreciated. >> Many thanks in advance. >> Best Regards, >> Angelica >> > > >-------------------------------------------------------------------------- - >Stephen M. Smith, Professor of Biomedical Engineering >Associate Director, Oxford University FMRIB Centre > >FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >+44 (0) 1865 222726 (fax 222717) >[log in to unmask] http://www.fmrib.ox.ac.uk/~steve >-------------------------------------------------------------------------- -