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If you only use only the thalamic seed and cortical target in one hemisphere, I would be surprised if you got much in the other hemisphere. If you still have that issue, even when using the white matter mask below, you could put a single slice mask across the corpus callosum and call it with the -avoid argument (I think this is exclusion in the GUI?). Peace, Matt. _____ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Marenco, Stefano (NIH/NIMH) [E] Sent: Wednesday, March 25, 2009 1:45 PM To: [log in to unmask] Subject: Re: [FSL] probtrackx and thalamocortical tracts I am trying to detect only the tract between the thalamus and the PFC. I will run the program again as a single seed mask (thalamus) and the PFC being the cortex. The other masks I would like to use are termination or exclusion masks to constrain further the fibertracking (e.g. to one hemisphere). Stefano _____ From: Matt Glasser [mailto:[log in to unmask]] Sent: Wednesday, March 25, 2009 1:04 PM To: [log in to unmask] Subject: Re: [FSL] probtrackx and thalamocortical tracts I think you don't want multiple masks in this case, you just want the thalamic seed and cortical target (or waypoint) (this is based on what you said in the first e-mail). Now you are talking about three masks, and I'm unclear what it is you are trying to do. Can you explain exactly what tracts you are hoping to find, and how they will pass through the masks you are using? Peace, Matt. _____ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Marenco, Stefano (NIH/NIMH) [E] Sent: Wednesday, March 25, 2009 11:52 AM To: [log in to unmask] Subject: Re: [FSL] probtrackx and thalamocortical tracts Hi Matt and other tractography experts, I like your suggestion for the white matter mask, and maybe the easiest way to resolve both of my questions is to cut that mask further behind and below the thalamus to avoid stray samples from continuing into unwanted territory. However, I am going to ask a few more questions about doing the tractography below. I think your other suggestion of seed in thalamus and target in ctx does not work, as the tract extends behind the thalamus, thus further termination masks may be necessary. I did this by using the gui and selecting multiple masks, listing the thalamic and frontal cortex masks as seeds and the prefrontal cortex as termination mask. I would not use exclusion masks because those would eliminate the whole length of the sample extending from thalamus to dlpfc and propagating behind and below the thalamus. Is this last statement correct? Another question I have is whether by specifying two masks, probtrackx does tractography using both of these independently as seeds, but maybe no tracts will emerge from the prefrontal cortex mask because it is also specified as a termination mask. One other problem is that only one termination mask is allowed in multiple masks tractography, at least in the gui. Would it be possible to use further termination masks when using the command line? The normalization remains an issue, as with multiple masks tractography the waytotal is not created, I think (at least I don't see it in my output dir).. So the only way is to use the first solution. In the case that I mentioned above, the max value I get is 18329, somewhere in the thalamus. I would expect this voxel to have a fairly high probability of connection after normalization (e.g. 0.9), but given 280 voxels in the thalamic mask, 6309 in the PFC mask and 5000 samples per voxel, it seems that this would not be the case at all. So I am sure I am doing something wrong, I am just not sure what or how I should prescribe the tractography. Any help is appreciated. Stefano Marenco _____ From: Matt Glasser [mailto:[log in to unmask]] Sent: Monday, March 23, 2009 4:51 PM To: [log in to unmask] Subject: Re: [FSL] probtrackx and thalamocortical tracts Well regarding your second question, you could segment the white matter using your structural image using FAST or other segmentation method, make a mask containing only the white matter, transform it to diffusion space using FLIRT and -interp nearestneighbour, and use that instead of nodif_brain_mask. I do this all the time (with segmentations generated from FreeSurfer white matter surfaces) and I get much cleaner tractography results as a consequence. If you put your seed in the thalamus and your target in the cortex, you should avoid pathways going beyond the thalamus. As far as normalizing your probability values, you can either divide by the total number of samples you send out (# of samples per voxel X number of voxels) or by the number of samples that reach the target (the waytotal), depending on what you want to show. I have found that the first method shows hemispheric asymmetries better, whereas the second method gives a more consistent pathway size across hemispheres and subjects. Peace, Matt. _____ From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Marenco, Stefano (NIH/NIMH) [E] Sent: Monday, March 23, 2009 3:40 PM To: [log in to unmask] Subject: [FSL] probtrackx and thalamocortical tracts I have two masks: one in the thalamus and the other in the cortex and I want to identify the tract that connects these two masks, nothing more. Is there a way to do this without creating termination or exclusion masks below and behind the thalamus? Is there a way to do this that would avoid assigning very low but non-zero values to the gray matter and /or CSF near the white matter? In the case where I would need to threshold the resulting probabilities in order to exclude gray matter or CSF (say pick voxels with 90% probability of belonging to the tract), if I were running probtrackx in multiple masks mode, would it be sufficient to divide by the resulting image by the total number of voxels in the two seedmasks to obtain reasonable probability values? Stefano Marenco, MD NIMH/GCAP Building 10, room 3C104 10 Center Drive Bethesda, MD 20892 tel 301 435-8964 fax 301 480-7795 email: <mailto:[log in to unmask]> [log in to unmask]