Organizing some GE scanner data into BIDS format, in order to run it through FMRIPREP, and running into the following issues:
Each subject has several func runs, and each func run has two associated fmap images (
magnitude.nii) in the fmap directory as follows (example screenshot of one subject):
The func directory has all the corresponding functional images.
I get the following error on BIDS Validator:
I can temporarily fix issue #1 by removing
phasediff.niifilenames (although according to the BIDS specification document, keeping
run-restpreshould be fine, right?), but then I can only have one set of fieldmap images for all the func images, so issue #1 still needs to be fixed - any suggestions?. Now after my temporary fix of issue #1, I run BIDS validator and get the following error regarding the
Here’s what my
I can only include one
EchoTimebecause dual echo times were not collected to do the correction, here it’s just the same echo time but instead reverse the phase encoding direction was used to calculate the distortions. I tried to ameliorate this error by including 80ms as both
.json, but get the following error:
So it seems that I can’t have two
EchoTimevalues, what is the solution to this?
Moreover, I get a BIDS Validator error that says
qform_codein the header are zero values, see below:
mri_info(from FreeSurfer) to obtain header information on the
phasediff.niiimages, and here are the respective screenshots:
Do I have to modify anything in the headers of
magnitude.niiimages to get them BIDS validated?