I have now completed the “Diffusion image processing” steps with success. I now get a new error at step 2 of the “Connectome generation” (SIFT).
tcksift 100M.tck WM_FODs.mif 10M_SIFT.tck -act 5TT.mif -term_number 10M
tcksift: [100%] resampling ACT 5TT image to fixel image space
tcksift: [100%] segmenting FODs
tcksift: [100%] mapping tracks to image
tcksift: [ERROR] Filtering failed; desired number of filtered streamlines is greater than or equal to the size of the input dataset
I tried without the last option and it worked, but the subsequent step seems to produce a corrupted file:
$ tcksift 100M.tck WM_FODs.mif 10M_SIFT.tck -act 5TT.mif
tcksift: [100%] resampling ACT 5TT image to fixel image space
tcksift: [100%] segmenting FODs
tcksift: [100%] mapping tracks to image
tcksift: Iteration Removed Remaining Cost fn
tcksift: [done]
tcksift: [100%] Writing filtered tracks output file
$ tck2connectome 10M_SIFT.tck nodes_fixSGM.mif connectome.csv
tck2connectome: [100%] Constructing connectome
tck2connectome: [WARNING] The following nodes do not have any streamlines assigned:
tck2connectome: [WARNING] 2, 5, 9, 11, 12, 15, 24, 25, 31, 32, 33, 39, 42, 43, 47, 48, 49, 50, 51, 54, 58, 61, 62, 63, 64, 65, 71, 74, 80, 81, 82
tck2connectome: [WARNING] (This may indicate a poor registration)
$ mrview nodes_fixSGM.mif -connectome.init nodes_fixSGM.mif -connectome.load connectome.csv
mrview: [ERROR] Input parcellation image must have an integer datatype; try running mrconvert -datatype uint32
mrview: [ERROR] Connectome matrix contains 84 nodes; expected 0
Thanks for your help.
Thanks for the advice. To clarify, it’s a collegue of mine that will be doing the analysis and she knows this kind of stuff and knows about the HCP data. Since I have a more powerful laptop, I am in charge of the generation of the connectome.