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yeatmanlab / AFQ

Automated Fiber Quantification
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Nan value in FA matrix #30

Open jinyika opened 5 years ago

jinyika commented 5 years ago

I am facing the similar NaN issue, mainly from the bilateral Hippocampal Cingulum tracts. The missing data were as high as 50% even in my control adult dataset. I have inspected them by overlaying the pair of ROIs and the cleaned FG on dtiFiberUI. It seems like those hippocampal cingulum fibers can be tracked separately from ROI1 or ROI2, but not "long enough" to touch both ROI waypoints in the subjects with NaN. Therefore it returned out no fibers for these 2 tracts. Since the NaN are far more than those from right AF, I am wondering whether it's common. How can I dealt with it? Shall I completely get rid of the Hippocampal Cingulum tracts for everybody from the 20 fibers?

Thanks. Cheng

ShuyueWang commented 4 years ago

Hi jinyika, I seem to have a similar issue, that FA results of test data computed from dtiComputerFA.m were all NAN. And the example code then stopped at AFQ_WholebrainTractography.m, and the error was in dtiClean (roiMask = zeros(diff(bb)+1)) : error using zeros, size vector must be a row vector with real element. Strangely, I ran example.m without any problems few months ago......Even weirder, sometimes it's ok (I did not change anything). I wonder if your problem has been solved since then. I am apprecaite if you could provide any suggestion. Thanks in advance!

ZhongNans commented 4 years ago

Hi jinyika, I seem to have a similar issue, that FA results of test data computed from dtiComputerFA.m were all NAN. And the example code then stopped at AFQ_WholebrainTractography.m, and the error was in dtiClean (roiMask = zeros(diff(bb)+1)) : error using zeros, size vector must be a row vector with real element. Strangely, I ran example.m without any problems few months ago......Even weirder, sometimes it's ok (I did not change anything). I wonder if your problem has been solved since then. I am apprecaite if you could provide any suggestion. Thanks in advance!

I also encounter such problems from time to time, so I did not use his algorithm for the fiber tracking part, but I cannot generate dt6 now, do you have any suggestions?