User Guide¶
Contents¶
Dependencies¶
If you are using a linux distribution with neurodebian, installation should be as easy as:
sudo apt-get fsl afni ants
sudo ln -sf /usr/lib/ants/N4BiasFieldCorrection /usr/local/bin/
After installation, make sure that all the necessary binaries are added to the $PATH
environment
variable, for the profile used run mriqc
.
Otherwise, you can follow each software installation guide: FSL, AFNI, and ANTs.
Running mriqc¶
The software automatically finds the data the input folder if it follows the BIDS standard [BIDS]. A fast and easy way to check that your dataset fulfills the BIDS standard is the BIDS validator.
Running mriqc
only requires:
mriqc -B ~/Data/bids_dataset -o out/ -w work/
It is possible to run mriqc
on specific subjects using
mriqc -B ~/Data/bids_dataset -S S001 S002 -o out/ -w work/
where S001
and S002
are subject identifiers, corresponding to the folders
sub-S001
and sub-S002
in the BIDS tree. Here, it is also accepted to use the sub-
prefix
mriqc -B ~/Data/bids_dataset -S sub-S001 sub-S002 -o out/ -w work/
Depending on the input images, the resulting outputs will vary as described next.