Hi FSL experts,
I have finished analysis of FA in TBSS, and clusters is :
Cluster Index Voxels MAX MAX X (mm) MAX Y (mm) MAX Z (mm) COG X (mm) COG Y (mm) COG Z (mm)
6 1110 0.918 -11 30 10 -3.56 25.7 15.6
5 594 0.912 -28 34 0 -28.4 32.9 7.36
4 43 0.901 16 -1 35 16 -0.349 35.5
3 39 0.9 10 -1 29 10.5 -2.28 29.9
2 37 0.901 8 -8 37 8.22 -8.49 35.3
1 5 0.9 13 -15 31 12.4 -13.6 31.6
Next , I used JHU-ICBM-DTI -81 white matter labels and Juelich Histological to label clusters with significant FA alterations in Fslview .
I scoured mailing list ,but still confused at some questions .
1. What's the difference between JHU and Juelich?Because they label different structure ,as shown in Fig.1 .
I should report the JHU, is right ?
2. Simestimes the JHU display "unclassfied" , what can I do ?
3. cluster -i tbss_tfce_corrp_tstat1.nii.gz -t 0.95, -o cluster_indices --osize=cluster_size > cluster_info.txt
i . In order to get cluster size >50 ,
fslmaths cluster_size -thr 50 -bin masked_size_over50
fslmaths tbss_tfce_corrp_tstat1.nii.gz -mul masked_size_over50 tbss_tfce_corrp_over50_tstat1
But when adding tbss_tfce_corrp_over50_tstat1 ,fslview did't display significant difference .Why ?
ii. extracting mean FA of a significant difference region (e.g Genu of corpus callosum,its peak coordinate -11,30,10,
cluster index 6 as shown above) :
fslmaths /usr/local/fsl/data/atlases/JHU/JHU-WhiteMatter-labels-1mm.nii.gz -thr 3 -uthr 3 -bin -mul
tbss_tfce_corrp_tstat1.nii.gz -thr 0.95 -bin masked_tfce__GCC
(maybe it could be in such:
fslmaths cluster_indices.nii.gz -thr 6 -uthr 6 -bin cluster_number6.nii.gz
is right ?
)
fslmeants -i tbss_tfce_corrp_tstat1.nii.gz -m masked_tfce_GCC -o meantsGCC.txt
(maybe it could be in such:
fslstats tbss_tfce_corrp_tstat1.nii.gz -k masked_tfce_GCC –m
is right ?
)
Then how to extract a single FA of Genu of corpus callosum ,not mean ?
Say sorry for bothering everyone .
Many regards.
Xin-Fa Shi.
|