Dear FSL expert,
This is the first time that I am doing tractagraphy and I really need your help.
I want to find the pathway between corpus callosum and visual cortex.
I made a mask for corpus callosum based on JHU atlas which the mask is in the standard space.
I previously ran VBM and find some significant area with changes in GM density in visual cortex. I manually made a mask from that. As this was from VBM stat results and all VBM results, as I think, is in standard space because of the registration to standard space therefore this mask should be in standard space. Is it right?
Now I ran probtarckx. I put my VBM mask which is in standard space as my seed point and I chose " the seed point is not in the diffusion space" and I put the matrix "standard2diff.mat" in xfms.
For my target, I chose waypoints and I put the corpus callosum mask there.
Well, as I read the tutorial, it was mentioned that seed point and target should be in the same space. So now my question is: As my VBM mask is in standard space and I used the transforming matrix to transform it to diffusion space, should I use flirt to register my corpus callusom mask from standard space to diffusion as well and then put this new corpus2diff mak in my way poin target?? OR I do not need to do that and I can put corpus callosum mask in standard space as my target???
My next question is when I get the result, is the fdt_path.nii.gz the one that I should look to see the tracts??
I also have other questions which might look some how dummy but I need to ask.
When I look through fdt_path.nii.gz,there are tons of tracts but not from my seed to target!!!!!! and when I put min to 0.95 it would not limited or it is better to say that there is no change in the number of tracts?! Is there something wrong?!?!
And also I can't see the tracts as the one that it is shown in the tutorial! Am I doing something wrong? Or I should change someting to see the tracts???
I would highly appreciate to help me in this regard,
Thank you in advance,
Gelareh
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