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
>>
>
>
>--------------------------------------------------------------------------
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>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
>--------------------------------------------------------------------------
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