Re the tractography practical, I am uncertain as to how to calculate the probability of connection between seed mask (here the right thalamus) and target cortical mask. I don’t have much experience with FSL, so I apologize in advance for the likely simplistic nature of this question.
Specifically, in this segment (Connectivity-based segmentation: http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/fdt2/index.html#conseg ), we are asked to “compare the spatial distributions and probabilities of connection from different thalamic voxels to different cortical target zones” for this subject.
Looking at the output (seeds_to_* files) with fslstats (e.g. fslstats seeds_to_MASK_average_M1_right.nii.gz -V 716 5728.000000; fslstats seeds_to_MASK_average_temporal_right.nii.gz -V 1109 8872.0000000) the voxel values showing the highest number of samples reaching the target mask come from the seeds_to_MASK_average_temporal_right.nii.gz image; this image is listed as the 7th out of 7 after running the find_the_biggest call. I would have thought that (reciprocal) connections between the right thalamus and M1 would be greater?
It’s apparent that the pro_thresh command is used to arrive at the probabilities of connection between the seed mask (proj_thresh <lots of volumes/surfaces> threshold), but what should the threshold be 50, 100, 500?. I assume this will be (fractions) out of 5000? If example usage for this data (fdt2/subj1.bedpostX/THAL2CTX_right) could be provided it would be greatly appreciated.
Best,
Lance
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