BIDS lesion mask specification

bids

#1

Hi all,

I’m working on a couple longitudinal studies which use manually drawn lesion masks. I’m having a hard time getting the data organized correctly in BIDS (1.0.1) with this setup (multiple sessions/T1s, only one lesion mask) and am a bit confused about how the mask needs to be specified.

From the fmriprep documentation page, I thought it just needed to be in the same directory as the T1 like this:
sub-x
ses-y
anat
sub-x_ses-y_T1w.nii
sub-x_ses-y_T1w_label-lesion_roi.nii

From the BIDS extension documentation I got the impression that I needed it to go in a separate derivatives/ parent folder and/or have the _space-orig delineation, but I haven’t been able to find a combination of any of the options I came across that would pass validation via http://bids-standard.github.io/bids-validator/.

Is this setup possible (would like to create an unbiased T1 and incorporate the one mask for normalization), and if so how?

Sorry if I’m missing something obvious, the documentation is thorough so I’m sure that’s the case.

Thank you!
James


#2

Hi James

yes, lesions should go into derivatives, is this combination works?:
sub-x
ses-y
anat
sub-x_ses-y_T1w.nii

derivatives/sub-x
derivatives/ses-y
derivatives/anat
derivatives/sub-x_ses-y_T1w_label-lesion_roi.nii

cyril


#3

Hi James,

Lesion masks are one place we haven’t updated fMRIPrep to conform to the BIDS Derivatives release candidate. For now, you should use the old filename, which I believe should still work.

Chris