Kyota-exe
commented
8 months ago 1179b35 has "flattened" the output directory of the script (the generated BIDS database) so that all sites are included as separate versions of each subject in accordance with option 2 described in this article. After having sorted all the NYU DICOMs, I've also added NYU to the list of sites that the script supports with 3986165.
The following is now the list of directories that the script generates:
sub-MGHd/
sub-MGHl/
sub-MGHr/
sub-MGHspinoza6/
sub-MNId/
sub-MNIl/
sub-MNIr/
sub-MNIspinoza6/
sub-NYUd/
sub-NYUl/
sub-NYUr/
jcohenadad
evaalonsoortiz
vcallot
This script converts the existing data for MGH and MNI scans from the previous structure/format to BIDS.
In order to use it, first download the archives from the OSF repository, unzip them and rename them to
SITE-original. Then run thebids_conversion.pyscript from this directory. It will generate a folder calledoutputs, which has the following directory structure:This is an example of the
treeoutput forMGH/SubD:I followed the general instructions detailed in #8 to figure out in which directory (
fmaporanat) to place each file, but did not know how to name every file. I thus named them so that it clearly states the relevant information that distinguishes each file, and added the series number when I wasn't sure what exactly differentiates them (for example, for the GRE combined scans or the DREAM scans). For the DREAM scans for which we were not sure which ones to include/exclude, I simply included all of them as a first step, but it will be easy to modify this as needed. Now that the script is written, it is very easy to rename these files correctly so they follow the BIDS convention.I would appreciate guidance concerning what the correct naming convention should be for these files. I have uploaded the generated outputs from this first version of the script in NeuroPoly/Projects/Spine7T_Zurich/Data/outputs_2023-12-27.zip.