Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Update docs #239

Merged
merged 1 commit into from
Jul 17, 2023
Merged

Update docs #239

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
21 changes: 17 additions & 4 deletions docs/tutorial/first-steps.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -336,6 +336,11 @@ To download the data, you can use your terminal or the GitHub interface. You can
do it any way you want as long as the directory with the dicoms is in
**sourcedata** directory with the name **dcm_qa_nih**.

In general, dicoms are considered sourcedata and should be placed in the
**sourcedata** directory. There is no explicit BIDS organization for **sourcedata**,
but having all of a subject's dicoms in a folder with the subject's name is
an intuitive organization (with sub-folders for sessions, as necessary).

=== "Terminal"

=== "Commands"
Expand Down Expand Up @@ -511,10 +516,11 @@ the command, the current directory.

!!! tip "Use one participant only"

For this tutorial, it is easy since you there are only few data. However, in
project with many participants, it is recommended to use data from one
one session of one participant only by targeting their directory, otherwise you may be overwhelmed
by the number of files for nothing.
For this tutorial, it is easy since there are only few data. However, in
general, each folder of dicoms should be specific to a participant and session.
This will not only be more computationally efficient, but also avoid any
confusion with overlapping file names between sessions if protocols are
repeated.

In this tutorial, there are two directories with data, one with data coming from a
Siemens scanner (`20180918Si`), and one with data coming from GE (20180918GE).
Expand Down Expand Up @@ -930,6 +936,13 @@ task name:
the [release notes of version 17-March-2021 (v1.0.20210317)][dcm2niix-release]
of dcmniix to now more, especially the [GE file naming behavior changes (%p protocol name and %d description) section](https://github.com/rordenlab/dcm2niix/issues/476).

!!! warning "Use SeriesNumber with caution"

It is not uncommon for runs to be repeated due to motion or the participant
leaving the scanner to take a break (leading to an extra Scout acquisition).
This will throw off the scan order for all subsequent acquisitions,
potentially invalidating several matching criteria.

Moving to the fieldmaps, if you inspect their sidecar files (the same ones that
were compared in the
[dcm2bids_helper section](#finding-what-you-need-in-tmpdcm2bidshelper)), you can
Expand Down