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 (
phasediff.nii
andmagnitude.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
run-restpre
from themagnitude.nii
andphasediff.nii
filenames (although according to the BIDS specification document, keepingrun-restpre
should 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.json
file:
Here’s what my.json
file says:
I can only include oneEchoTime
because 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 bothEchoTime1
andEchoTime2
in the.json
, but get the following error:
So it seems that I can’t have twoEchoTime
values, what is the solution to this? -
Moreover, I get a BIDS Validator error that says
sform_code
andqform_code
in the header are zero values, see below:
I ranmri_info
(from FreeSurfer) to obtain header information on themagnitude.nii
andphasediff.nii
images, and here are the respective screenshots:
Do I have to modify anything in the headers ofphasediff.nii
andmagnitude.nii
images to get them BIDS validated?