Closed finnlennartsson closed 1 year ago
This has been updated now in 7b0829e. The cat12
command now runs as it should but the output files stays in the cat12 folder. Todo:
Move files to raw data
.../cat12/sub-XXX_desc-pymp2ragecat12_T1w.nii.gz
to
raw data/sub<X>/anat/sub-XXX_rec-pymp2rageCat12_UNIT1.nii.gz
Note how we have swapped from desc
to rec
which stands for reconstruction.
Copy over the corresponding .json sidecar.
This new file must be added into studydir/rawdata/sub-XXX/sub-XXX_scans.tsv
.
This has now been completed with 6ceef5d2cb6f1fb6a0363952112050454dd0d62b. Axel has implemented that the new file gets copied to rawdata/sub<X>/anat/sub-XXX_rec-pymp2rageCat12_UNIT1.nii.gz
. The json sidecar is also included and the new file is added to the scans.tsv file.
Axel's pipeline is a replica of the Knapen Lab's anatomical workflows.
There is an important difference though. In the original pipeline, the output should be a denoised T1w image (both background and internal noise removal). Axel's pipeline is outputting a denoised but skull-stripped T1w image.
The recommendation from fMRIprep is not to use a skull-stripped image. See point in FAQ and relevant neurostars issues related to this (see links in FAQ entry).