Dear FSL expert,
I used the FDT, bedpostX and probtrack( Seed and waypoint) for DTI tractagrophy and got the result as fdt_paths.nii.gz. In order to find better pathway I thresholded the result and then binarised it to make a mask. Now there are two issues:
1-In order to do my tractagraphy I used structrual images and in probtrack I ticked the box which was mentioned the mask was not in diffusion space and I put the matrix for transferring structure to diff. So I assume that now the result would be in diffusion area, isn't it ?
2- In order to find the mean FA of the path that I found, I think that I should take the afore-mentioned mask and put it in my FA image which was registred to MNI space before (as I have so many subjects and I want to do comparison). so I used below script:
fslstats my_FA_image -k my_mask -M>> mean_FA.txt
But it told me that the size of mask and image should be the same.
The size of image is: 1*1*1mm
The size of mask is : 0.8* 0.78125*0.78125mm
I am wondering what should I have to do with the mask!??!!
Is the mask in the diffusion space or structrual image!?
I assume that My FA images which was registered to MNI space are now in standard space so should I use flirt to transfer the mask from diff to standard space??? Although when I try this:
flirt -in my_mask -ref MNI152_T1_1mm_brain applyxfm -init matrix.mat -out my_output
I mean use flirt to find matrix to transfer diff to standard 1mm and then use the flirt and applyxfm to have the transferred image, this message appears "unrecognised option a". What does this mean!?!? So where is the problem then!?
I would highly appreciate if you could help me and give me a hint.
Best Regards,
Gelareh
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