Hi Eddy
> 1)I must work in MNI space, I do run tbss_2_reg -T for this. when I
> find the
> eigenvectors must be mediated in the new space, I do:
>
> ->vecreg -i PAZIENTE_0_V1 -o PAZIENTE_0_V1_warp -w
> PAZIENTE_0_FA_FA_to_target_warp -r mean_FA (is corect
> usemean_FA as
> refer?)
>
> I bring vector in new space MNI, is right?
yes.
> then I apply the steps that I you told me:
>
> -> fslmaths PAZIENTE_1_V1_warp -mul PAZIENTE_0_V1_warp -Tmean -div 3
> V1_dot
> ->fslmaths V1_dot -abs -div V1_dot V1_sign
> ->fslmaths PAZIENTE_1_V1_warp -mul V1_sign PAZIENTE_1_V1_reor
> ...
> ->fslmaths PAZIENTE_0_V1_warp -add PAZIENTE_1_V1_reor -add
> PAZIENTE_2_V1_reor -add PAZIENTE_3_V1_reor -add PAZIENTE_4_V1_reor -
> div 4
> V1_average
>
> This is ok..but, there is a more refined method of averages to find
> the
> eigenvectors in the new space? when I use fslview and module
> V1_average on
> mean_FA , I hope of finding a better result.
a better way to do it is to calculate the average tensor, and extract
its first eigenvector (which would give you something like the "mode"
rather than the mean).
>
>
> 2)when I use the second part, that is, when I calculate the tensor
> elements:
>
> ->fslsplit mean_V1 V1
> ->fslsplit mean_V2 V2
> ->fslsplit mean_V3 V3
> ->fslmaths mean_L1_skeleton.nii.gz -mul V10000.nii.gz -mul
> V1000.nii.gz tmp1
> ->fslmaths mean_L2_skeleton.nii.gz -mul V20000.nii.gz -mul
> V2000.nii.gz tmp2
> ->fslmaths mean_L3_skeleton.nii.gz -mul V30000.nii.gz -mul
> V3000.nii.gz tmp3
> ->fslmaths tmp1 -add tmp2 -add tmp3 tensor11
>
> the system give me an error:
>
> fslmaths all_L1_skeletonised.nii.gz -mul V10000.nii.gz -mul
> V1000.nii.gz tmp1
> ** ERROR (nifti_image_read): failed to find header file for 'V1000'
> ** ERROR: nifti_image_open(V1000): bad header info
> Error: failed to open file V1000
> ERROR: Could not open image V1000
> Image Exception : #22 :: Failed to read volume V1000.nii.gz
> terminate called after throwing an instance of
> 'RBD_COMMON::BaseException'
> Aborted
>
my mistake: you need 4 zeros, not three!
So just type:
->fslmaths mean_L1_skeleton.nii.gz -mul V10000.nii.gz -mul
V10000.nii.gz tmp1
->fslmaths mean_L2_skeleton.nii.gz -mul V20000.nii.gz -mul
V20000.nii.gz tmp2
->fslmaths mean_L3_skeleton.nii.gz -mul V30000.nii.gz -mul
V30000.nii.gz tmp3
> Can you help me?
>
> Thanks
>
> Eddy
>
Saad Jbabdi
Oxford University FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
+44 (0) 1865 222545 (fax 717)
www.fmrib.ox.ac.uk/~saad
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