tutorials improvs
The following comments and suggestions refer to the files contained in the tutorials folder
README.md -
- could be useful to add a few lines on preliminary knowledge skills that are requested to the user to run the tutorial
01_installation.ipynb -
- Jupyterlab is cited, but no prior mention of it in tutorials' readme file; for consistency (and for noobs) either change to jupyter notebook or, if jupyterlab is recommended, add instruction on installation in readme file, e.g. https://jupyterlab.readthedocs.io/en/stable/getting_started/installation.html
03_basic_mapping.ipynb -
second cell:
-
could be useful reporting, here or in main readme file, the list of attributes that should be filled as 'mandatory', 'optional' etc. in the bidsmap file to obtain a bids-conform name of the subject (for each modality)
-
what is "block"? this is not defined elsewhere; important to specify so that the user knows how many sections of the mapping file will be generated
-
suffix: is this set automatically by bidsme, or should the user specify it based on BIDSstandards documentation?
-
line 29-35: are these also automatically retrieved by bidsme based on folder name?
third to last cell:
-
in my run, the subject is reported in the maps file as anat/sub-Sub001_ses-s01530_acq-placeholder_echo-1_MPM and not as anat/sub-001_ses-s01530_acq-placeholder_echo-1_MPM , as indicated in the example
-
line 16: 'At this point, you can change
template
fromtrue
tofalse
for modified blocks, and rerunbidsme map
' please explain why this is done at this point - is it because we expect no more errors? This was not done in the previous attempt at dealing with errors. What is the effect of not changing template from T to F?