Hi. I’m following the ‘Fibre density and cross section -Multi tissue CSD’ tutorial. I’ve finished running through the entire pipeline just to discover that almost all the files are mostly empty (they do have 1-10 random voxels with values). The only exceptions are the index.mif files that at all stages of the pipeline show the brain. When I try to find where the error is I found out that the first file that is empty is the fd.mif file that is generated in step 14 for each subject (in the directory fixel_in_template_space_NOT_REORIENTED). I also did notice that the files subject2template_warp.mif and template2subject_warp.mif seem funky in mrview (see attached image - maybe this could be the problem). Any ideas on how to proceed?
Hello, I have a similar problem except fod2fixel does not output anything and stops after segmenting in my case and my template_mask.mif is an empty image so my problem is likely different.
My warp files do look the same as in this thread though so I would be grateful if someone could confirm that’s the way they are supposed to look.