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 noticed that the files subject2template_warp.mif and template2subject_warp.mif seem funky in mrview (see attached image - maybe this could be the problem).
Hi @polivaoren ,
Would you please load wmfod.mif in mrview & under tools, you will have fixel plot, maybe you can drag your fd.mif there. I hope that’s not empty.
You may also check mrstats fd.mif. I hope you get some values as outcome.
Also if you like to see fd.mif in mrview, you can use fixel2voxel fd.mif mean fd_mean.mif. I hope it’s not empty.
Great. I was using overlay. When I used fixel plot instead, I can see the data. New question: which of the many files am I expected to look at for a group comparison (zstat, fwe, tstat etc)? I can’t find any location in the documentation that elaborate on that.
These are basic statistical values for the GLM contrast you perform, at each fixel:
Zstat = Z value (population statistic)
Tstat = T value (sample statistic)
fwe = 1 - family-wise error corrected p-value
Is the zstat corrected for family wise error? Can we use it for thresholding (I noticed it automatically appears in the thresholding section of the fixel tool)? or do I use the cfe file for thresholding (and if yes, how do I do the thresholding given the high values)?
Have answered in the other post - but just to be clear, the Z value is just an effect size, it does not say anything about the likelihood of finding that effect size if the null hypothesis is true.
