Hi,
On 10 Feb 2009, at 08:20, Yuzheng HU wrote:
> Dear FSL users,
> I have used FSL for DTI analysis, but I am not sure whether all the
> steps in
> my procedure are appropriate. So I would appreciate you very much if
> someone can help me to check it. There are two groups in my
> experiment and
> 25 subjects in each. My research purpose is to compare the difference
> between the two groups in FA and skeletonised FA. Please see my
> procedures
> for this purpose as follow.
> #Section 1, tensor estimation for each subject in his/her own
> directory
> eddy_correct DTI_raw.nii.gz data 0
> bet data.nii.gz nodif_brain_mask
> dtifit -k data -o dti -m nodif_brain_mask -r *.nii.bvec -b *.nii.bval
> # estimation end
> # Section 2, TBSS analysis
> # copy and rename dti_FA.nii.gz from each subject`s folder to the
> same dir.
> e.g. ‘./TBSS’
> # cd to ./TBSS
> tbss_1_preproc *FA*.nii.gz
> tbss_2_reg -T
> tbss_3_postreg -S
> tbss_4_prestats 0.2
> cd stats
> design_ttest2 design 25 25
> randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d
> design.mat -t design.con -c 1.6839 –V
> # mean difference at the significant level of p < 0.05 is expected.
> Option –c
> is used with a value of 1.6839 by looking up t-value tables,
> t0.05(42-2)
> =1.6839. Is this setting correct?
This is all ok - you would then look in maxc images to see where
cluster p-values of <0.05 (intensities of >0.95) corrected-p survive
testing. Alternatively I would recommend using the TFCE option (--T2)
instead of cluster-based thresholding in randomise.
>
> # TBSS end
>
> # Section 3, statistic for raw FA in ‘TBSS/stas’ directory
> # could I compare FA in the whole brain between groups directly with
> randomise command as flow?
> # threshold FA data by 0.2
> fslmaths mean_FA.nii.gz –thr 0.2 mean_FA_mask_2.nii.gz fslmaths
> # make a binary mask
> mean_FA_mask_2.nii.gz –bin mean_FA_mask_2_bin.nii.gz
> #make inference, is this appropriate as follow?
> randomise -i all_FA -o FA2 -m mean_FA_mask_2_bin -d design.mat
> -t
> design.con -c 1.6839 –V
> # statistic for FA end
You mean you want to compare the mean-across-space values in the
groups? Not quite, not, I would apply the mask (that's already done
for you hence doesn't appear below) and then summarise over space, e.g.
fslmaths all_FA_skeletonised -Xmean -Ymean -Zmean
global_FA_skeletonised
This results in a 4D file containing a timeseries of a single voxel.
You should be able to feed this into randomise with no extra options
(just -x) and just look at the uncorrected voxelwise p-value.
Cheers.
>
>
> Any suggestion is appreciated!
> All the best!
>
> Yuzheng.Hu
>
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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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