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[DOC] Improve
t1-linear documentation (#1429)
* Modify T1_Linear doc * Fix snippet * Try options in toggle-down * From sections to list * Fix new snippet * tsv option * Test1 * Test2 * Test3 * Test4 * Change working directory explanation * Put back space
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,43 +1,40 @@ | ||
| ## Common options for pipelines | ||
| - `-tsv` / `--subjects_sessions_tsv` | ||
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| ### `-tsv` / `--subjects_sessions_tsv` | ||
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| The `-tsv` flag allows you to specify in a TSV file the participants belonging to your subset. | ||
| This flag allows you to specify in a TSV file the participants belonging to your subset. | ||
| For instance, running the [FreeSurfer pipeline](/Pipelines/T1_FreeSurfer.md) on T1w MRI can be done using : | ||
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| ```shell | ||
| clinica run t1-freesurfer path/to/my/bids/dataset path/where/results/will/be/stored -tsv my_list_of_subjects.tsv | ||
| ``` | ||
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| where your TSV file looks as follows: | ||
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| ```text | ||
| participant_id session_id | ||
| sub-CLNC0001 ses-M000 | ||
| sub-CLNC0001 ses-M018 | ||
| sub-CLNC0002 ses-M000 | ||
| sub-CLNC0002 ses-M018 | ||
| sub-CLNC0003 ses-M000 | ||
| clinica run t1-freesurfer BIDS_PATH OUTPUT_PATH -tsv my_subjects.tsv | ||
| ``` | ||
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| !!! warning "Writing the TSV" | ||
| Note that to make the display clearer, the rows contain successive tabs, which should not happen in an actual TSV file. | ||
| <div class="grid" markdown> | ||
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| ### `-wd` / `--working_directory` | ||
| === "TSV Example :" | ||
| ```{ .text .copy } | ||
| participant_id session_id | ||
| sub-CLNC0001 ses-M000 | ||
| sub-CLNC0001 ses-M018 | ||
| sub-CLNC0002 ses-M000 | ||
| ``` | ||
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| !!! warning "Creating the TSV" | ||
| To make the display clearer the rows here contain successive tabs but that should not happen in an actual TSV. | ||
| </div> | ||
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| In every pipeline, a working directory can be specified. | ||
| This directory gathers all the inputs and outputs of the different steps of the pipeline. | ||
| It is then very useful for the debugging process. | ||
| It is specially useful in the case where your pipeline execution crashes and you relaunch it with the exact same parameters, allowing you to continue from the last successfully executed node. | ||
| - `-wd` / `--working_directory` | ||
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| !!! info "Working directory" | ||
| If you do not specify any working directory, a temporary one will be created, then deleted at the end if everything went well. | ||
| By default when running a pipeline, a temporary working directory is created. This directory stores all the intermediary inputs and outputs of the different steps of the pipeline. If everything goes well, the output directory is eventually created and the working directory is deleted. | ||
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| With this option, a working directory of your choice can be specified. It is very useful for the debugging process or if your pipeline crashes. Then, you can relaunch it with the exact same parameters which will allow you to continue from the last successfully executed node. | ||
| For the pipelines that generate many files, such as `dwi-preprocessing` (especially if you run it on multiple subjects), a specific drive/partition with enough space can be used to store the working directory. | ||
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| ### `-np` / `--n_procs` | ||
| - `-np` / `--n_procs` | ||
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| The `--n_procs` flag allows you to exploit several cores of your machine to run pipelines in parallel, which is very useful when dealing with numerous subjects and multiple sessions. | ||
| This flag allows you to exploit several cores of your machine to run pipelines in parallel, which is very useful when dealing with numerous subjects and multiple sessions. | ||
| Thanks to [Nipype](https://nipype.readthedocs.io/en/latest/), even for a single subject, a pipeline can be run in parallel by exploiting the cores available to process simultaneously independent sub-parts. | ||
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| If you do not specify `-np` / `--n_procs` flag, Clinica will detect the number of threads to run in parallel and propose the adequate number of threads to the user. | ||
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| - `-cn` / `--caps-name` | ||
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| Use this option if you want to specify the name of the CAPS dataset that will be used inside the `dataset_description.json` file, at the root of the CAPS folder (see [CAPS Specifications](../CAPS/Specifications.md#the-dataset_descriptionjson-file) for more details). This works if this CAPS dataset does not exist yet, otherwise the existing name will be kept. |