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Hi Nick So you are saying that streamlines from your patients show more spreading than controls, on the way to the cortex, but possibly not enough spreading to get significant differences in the streamline counts hitting the cortex. There are various ways you can quantify the spread: - overall tract volume (after thresholding) - tract width (per slice along the z-direction, as you will have more spreading for higher z coordinates in MNI space) - number of streamlines that reach other targets than sensori-motor whilst still starting from the seed voxels that have highest probability of connecting to the sensori-motor target Hope these help Saad On 26 Jun 2012, at 13:32, Nick Fallon wrote: > Dear Saad (or any other experts with ideas), > > I am conducting a connectivity analysis using probtrackx. I am interested in thalamo-cortical projections using thalamus seed masks, somatosensory cortex target masks and a spino-cortical waypoint mask. After performing my analysis and dividing my connectivity values by the appropriate waytotals I did not have a sig difference between groups in connectivity. However, upon evaluating the data, although connectivity to the target may not differ specifically, I have noticed that my patient group has a much more widespread connectivity matrix compared to controls.The masks I used appear to have successfully isolated thalamo-cortical projections in the appropriate tract in the control group but in my patient group I have involvement from other locations (not expected) at the same thresholds. I think the involvement of these different projections may indicate a significant difference in connectivity (not revealed by the number of samples reaching the target mask). > > I have checked my log files and I haven't made any errors: My question is can I somehow quantify the difference in the connectivity matrices using fslmaths (or anything else) to run statistics and quantify this difference? > > For instance, can they be projected onto skeleton templates used in TBSS and voxelwise statistics performed? If so I would appreciate any advice about how this can be done. > > Thanks in advance for any help or advice, it is much appreciated. > > Best, > > Nick > -- Saad Jbabdi University of Oxford, FMRIB Centre JR Hospital, Headington, OX3 9DU, UK (+44)1865-222466 (fax 717) www.fmrib.ox.ac.uk/~saad