Closed sxf-ux closed 1 year ago
Hi, if I am understanding, the EPI2ANAT you are showing corresponds to the latest outputs you obtained while using --bold2anat_coreg masking=true,brain_extraction=true,registration=Rigid
? In this case, you are only computing a rigid registration of your scan, so there won't be any non-linear warping to correct for distortions (you should keep the SyN option for non-linear). In the other call you have --bold2anat_coreg masking=false,brain_extraction=true,registration=SyN
, which carries out non-linear, but masking is at false, so the brain mask is not used to improve registration. Try --bold2anat_coreg masking=true,brain_extraction=true,registration=SyN
instead. Also keep in mind that the distortions in those images you are showing are very severe, and I would not expect a complete correction to be possible.
and what happens if I omit this epi2anat by doing no_reg
? what impact would this have downstream?
There would be no registration. The EPI image would retain its original positioning, dimensions and distortions.
Hello. I have been running my preprocessing pipeline and looking at the QC Report, my structural images appear to have run fine but my Functional EPI Images have not. I can't seem to find any information in the documentation as to why it would. Im running this with rat data and have inputted my own templates.
Here is the script I am using:
I initially ran the following but it crashed during 'EPI_Coregistration' so I added the
masking=true
andregistration=Rigid
for the bold2anat_coreg that you can see above:I adjusted the registration issue based on the recommendations on the rabies website which fixed my anatomical images. I also found that using robust_inho correction fixed my issue with my EPI images since previously, nothing registered and it was a blank image. Ive added my log and my QC Report for my EPI pipeline below (EPI2ANAT, temporal_features and bold inho corrections). Furthermore, I can't find any examples of failed EPI2Anat and what it means in my case and if what I have is a 'failure'. rabies_preprocess.log
bold_inho_cor
bold_robust_inho_cor (Native2Unbiased)
bold_robust_inho_cor (Unbiased2Atlas)
EPI2ANAT AT
temporal_features
Thank you in advance !