Dear XTRACT experts,
Could you please provide more information about the XTRACT output files? What is the difference among density_lengths.nii.gz, densityNorm.nii.gz and density.nii.gz?
We use ranomise to compare the ILF for two groups of subjects. Is the workflow described below correct?
1. First, we merged densityNorm.nii.gz files for all subjects for each specific tract.
fslmerge -t all_subjects_merged.nii.gz subj1/xtract/tracts/ilf_l/densityNorm.nii.gz subj2/xtract/tracts/ilf_l/densityNorm.nii.gz subj3/xtract/tracts/ilf_l/densityNorm.nii.gz etc.
2. Then we created design.mat and design.con files (the example below is for 6 subjects and reflects the order of subjects used in 'fslmerge')
==== design.mat ====
/NumWaves 2
/NumPoints 6
/PPheights 1.000000e+00 1.000000e+00
/Matrix
1.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00
1.000000e+00 0.000000e+00
0.000000e+00 1.000000e+00
0.000000e+00 1.000000e+00
0.000000e+00 1.000000e+00
===== design.con====
/ContrastName1 Gr1> Gr2
/ContrastName2 Gr2 > Gr1
/ContrastName3 Gr1 mean
/ContrastName4 Gr2 mean
/NumWaves 2
/NumContrasts 4
/PPheights 1.000000e+00 1.000000e+00 1.000000e+00 1.000000e+00
/Matrix
1.000000e+00 -1.000000e+00
-1.000000e+00 1.000000e+00
1.000000e+00 0.000000e+00
0.000000e+00 1.000000e+00
===============
3. Finally, we ran
randomise -i all_subjects_merged.nii.gz -o ilf_l_Gr1_vs_Gr2.nii.gz -d design.mat -t design.con --T2 -n 5000
We will appreciate your feedback.
Thank you very much,
Anna.
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