From be96522cfa597a3b54a37f333fe7963f76107232 Mon Sep 17 00:00:00 2001 From: Steven Meisler Date: Mon, 17 Jul 2023 14:30:41 -0400 Subject: [PATCH] Update first-steps.md --- docs/tutorial/first-steps.md | 21 +++++++++++++++++---- 1 file changed, 17 insertions(+), 4 deletions(-) diff --git a/docs/tutorial/first-steps.md b/docs/tutorial/first-steps.md index b44cd610..9601c848 100644 --- a/docs/tutorial/first-steps.md +++ b/docs/tutorial/first-steps.md @@ -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" @@ -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). @@ -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