Probtrackx always outputs results in the same space as the seeds are
specified in. You would either need to transform your seed and waypoint
masks into diffusion space or transform your results into diffusion space.
Peace,
Matt.
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf
Of Gelareh Ahmadi
Sent: Saturday, January 07, 2012 6:29 AM
To: [log in to unmask]
Subject: [FSL] Use the result of the tractography and finding its mean FA
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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