diff --git a/docs/container.rst b/docs/container.rst index 8ad96729..fd10d3a4 100644 --- a/docs/container.rst +++ b/docs/container.rst @@ -4,7 +4,7 @@ Using heudiconv in a Container If heudiconv is :ref:`installed via a Docker container `, you can run the commands in the following format:: - + docker run nipy/heudiconv:latest [heudiconv options] So a user running via container would check the version with this command:: @@ -46,4 +46,3 @@ We typically recommend users make use of the following flags to Docker and Podma * ``-it`` Interactive terminal * ``--rm`` Remove the changes to the container when it completes - diff --git a/docs/custom-heuristic.rst b/docs/custom-heuristic.rst index bfef79db..54299bbb 100644 --- a/docs/custom-heuristic.rst +++ b/docs/custom-heuristic.rst @@ -316,4 +316,3 @@ Suppose you want to use the values in the field ``image_type``? It is not a num Note that this differs from testing for a string because you cannot test for any substring (e.g., 'TEST' would not work). String tests will not work on a tuple datatype. .. Note:: *image_type* is described in the `DICOM specification `_ - diff --git a/docs/index.rst b/docs/index.rst index f17be802..2f63f524 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -19,4 +19,3 @@ Contents commandline container api - diff --git a/docs/quickstart.rst b/docs/quickstart.rst index 118c77dc..f52b905f 100644 --- a/docs/quickstart.rst +++ b/docs/quickstart.rst @@ -3,7 +3,7 @@ Quickstart This tutorial is based on `Dianne Patterson's University of Arizona tutorials `_ -This guide assumes you have already :ref:`installed heudiconv and dcm2niix ` and +This guide assumes you have already :ref:`installed heudiconv and dcm2niix ` and demonstrates how to use the heudiconv tool with a provided `heuristic.py` to convert DICOMS into the BIDS data structure. .. _prepare_dataset: @@ -11,7 +11,7 @@ demonstrates how to use the heudiconv tool with a provided `heuristic.py` to con Prepare Dataset *************** -Download and unzip `sub-219_dicom.zip `_. +Download and unzip `sub-219_dicom.zip `_. We will be working from a directory called MRIS. Under the MRIS directory is the *dicom* subdirectory: Under the subject number *219* the session *itbs* is nested. Each dicom sequence folder is nested under the session:: @@ -29,7 +29,7 @@ We will be working from a directory called MRIS. Under the MRIS directory is the ├── field_mapping_21 └── restingstate_18 Nifti - └── code + └── code └── heuristic1.py Basic Conversion @@ -57,36 +57,36 @@ Run the following command:: Output ****** - + The *Nifti* directory will contain a bids-compliant subject directory:: - - + + └── sub-219 └── ses-itbs ├── anat ├── dwi ├── fmap └── func - + The following required BIDS text files are also created in the Nifti directory. Details for filling in these skeleton text files can be found under `tabular files `_ in the BIDS specification:: - + CHANGES README dataset_description.json participants.json participants.tsv task-rest_bold.json - + Validation ********** -Ensure that everything is according to spec by using `bids validator `_ +Ensure that everything is according to spec by using `bids validator `_ Click `Choose File` and then select the *Nifti* directory. There should be no errors (though there are a couple of warnings). - + .. Note:: Your files are not uploaded to the BIDS validator, so there are no privacy concerns! - -Next + +Next **** In the following sections, you will modify *heuristic.py* yourself so you can test different options and understand how to work with your own data.