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Initialize derivative data set with a copy of the raw data #78
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I have also something similar in our lab pipeline though yours seem to have more features. I also know that spmup by @CPernet has something that does some of that. So that seems like one the obvious low hanging fruit !! |
Copied from original issue
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Actually had opened an issue on one of our repo to get spm_mkdir and spm_copy out of spm. So I would heart to have them as part of bids matlab. One headache to keep in mind: datasets curated with datalad have their content stored with git annex (I need to finish a PR about that on the datalad handbook). So a simple call to copyfile will not follow the symbolic link and you just end up with just a bunch of broken links. 2 options:
The second option is going to make Windows users cry though... If they use datalad: no a huge user base at the moment but that too could grow. Any other ways around this that would make everyone happy? |
Origianlly posted by @gllmflndn
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There are a few circumstances (see here under) where I would like to initialize the
derivatives
with a copy, complete or partial, of the original full BIDS dataset. I have been working on aprepare_derivatives.m
for that specific purpose with some features, such as:func
data possibly all or some tasks;.nii.gz
files and 4D-to-3D unpacking thefunc
anddwi
images, if requested;derivatives/tool
subfolder will be created, i.e. not necessarily next to the "raw" data in the BIDS folder.Why would I want to do that? Well because, it is convenient to work on a subset of data and/or in a "sandpit", for example
func
data), therefore no need to bring along everythingderivatives
subfolder before any processing. Moreover SPM and some other tools, would prefer dealing with a series of 3D images rather than a single 4D volume, e.g. ditching the 1st few functional images into a "dummy" subfolder.derivatives\some_tool_or_step
data and start working on these. Afterwards, it is straightforward to copy that derivatives folder back on the external storage place.Originally posted by @ChristophePhillips in #60 (comment)
dataset_description.json
in the root of that derivatiive folderSee comments:
In other repos:
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