Hi, @rsmith
Sorry for reviving such old threads. I have received the similar warning as this thread, since the number is relatively high (i.e. 200000+ fixels), so I tried to generated a mask according to your recommandation here. But I’m not familiar with MRtrix3, after searching relevant posts, I’m still don’t know how to write the command.
I run the tck2fixel below, and got the TDI.mif successfully, but when I tried to run the mrthreshold, I met errors. Could you please help me amend my commands? I’d very appreciate your help.
tck2fixel sift_2m.tck fixel_mask fixel_mask_tck2fixel TDI.mif
mrthreshold fixel_mask_tck2fixel/TDI.mif mask.mif
mrthreshold: [ERROR] Image "fixel_mask_tck2fixel/TDI.mif" does not represent spatial data (has axis with size 1)
mrthreshold: [ERROR] Automatic thresholding can only be performed for voxel data
Another message maybe useful, I viewed the TDI.mif, and there shows nothing.
BW,
Yuting