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>Would it be possible to send me your output fdt_network_matrix after adding option --pd? https://users.fmrib.ox.ac.uk/~moisesf/test_YING_NOpd.zip https://users.fmrib.ox.ac.uk/~moisesf/test_YING_YESpd.zip >Do you have any suggestion about how to adjust for the distance? They are different approaches, you probably do not want to do that >Last question is about the meaning of the data in the fdt_path.nii and fdt_path_length.nii..... Would it be possible to explain it? fdt_path: total number of streamlines that visited this voxel fdt_path_length: mean length of all streamlines when visited that voxel On Mon, 12 Nov 2018 at 21:51, Yingtian Hu <[log in to unmask]> wrote: > Hi Moises, > > I have tried to rerun the script. When using the option --ompl, I can > obtain the files ended with _lengths. However, the fdt_network_matrix does > not change no matter I add --pd or --ompl. Would it be possible to send me > your output fdt_network_matrix after adding option --pd? > > Additional question is that if I choose to obtain the probabilistic > tractography without using any of these options but dividing each > matrix-row by each waytotal-row, the calculated probabilistic actually has > not been adjusted for the distance. Do you have any suggestion about how to > adjust for the distance? > > Last question is about the meaning of the data in the fdt_path.nii and > fdt_path_length.nii. I know there are 3D image data of the path > distribution and path length. They can also be considered as large and > multiple dimension matrix. I am not sure what the meaning of each element > in those two matrix. Would it be possible to explain it? > > Thank you so much for your help. > > Sincerely, > Yingtian > > ----------------------- Previous Message ---------------------------------- > > With --pd option, the results are the sum of the length of all the > streamlines from ROI to ROI. > So, if there are 3 streamlines that go from A to B, with lengths > [20,30,20] mm, the result in the Matrix-cell A->B will be 70mm > With --ompl, will be 23.33mm (the mean) > Another approach is to normalize by the number of survival streamlines > from each ROI, i.e. without using any of these options but dividing each > matrix-row by each waytotal-row. > And another approach is to divide each Matrix-row by the size/area of each > ROI. > > Moises > > > On Wed, 31 Oct 2018 at 23:32, Yingtian Hu <[log in to unmask]> wrote: > Hi Moises, > > Thank you very much for your help. I will try to run the script again and > also the script with --ompl option. > > Another question is about the fdt_network_matrix. Based on my > understanding, the results in the fdt_network_matrix are the number of > streamlines connecting ROIs without option --pd. Now if we add option > --pd, the results in the fdt_network_matrix should be the corrected number > of streamlines. Is my understanding correct? > > Thank you very much. > > Sincerely, > Yingtian > > > To unsubscribe from the FSL list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1 > > ######################################################################## To unsubscribe from the FSL list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1