[Neuroimaging] using nibabel to convert a dtscalar parcellation (1-N for each greyordinate) to a 4d (binary slice for each parcel) dtseries
uri.urie at gmail.com
Sat Oct 24 14:05:58 EDT 2020
Top level - I'd like to apply dual regression on rest fMRI based on
parcellation where my rs-fMRI data in in CIFTI format.
For a dual-regression SW I've chosen FSL, also because it works on Cifti
(according to manual).
For parcellation I've chosen the Schaefer parcellation, as it is
Cifti-available and also partially based on rest-fMRI.
Now, the Cifti parcellation file is a dscalar file (that is - a single
volume/surface), with each greyordinate belongs to one of N parcels. FSL
(AFAIU) requires a 4D file as a reference
Working with nibabel, reformatting the matrix is easy - reading it with
nibabel and do something like: for k in range(N):
newdata[k,:] = (orgdata==k+1).astype(float)
Updating the Nifti header is also easy -
newobj = nb.Cifti2Image(newdata, dscobj.header, dscobj.nifti_header)
The problem with this way is the the Cifti header is not being updated -
What's a good way of doing this? - either by sticking to the nibabel->FSL
line right or by any alternative
Thanks all so much,
Computational Neuropsychiatry Lab
Hadassah Hebrew University Medical School
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