From ef5ceabb1e07be59e1a3fef15344bf0444310298 Mon Sep 17 00:00:00 2001 From: basile Date: Sat, 20 Jun 2020 21:26:33 -0400 Subject: [PATCH 1/6] list templateflow templates that need to be prefetched for fmriprep internal usage --- docs/faq.rst | 3 +++ 1 file changed, 3 insertions(+) diff --git a/docs/faq.rst b/docs/faq.rst index 6f4f04360..bc4ef6d25 100644 --- a/docs/faq.rst +++ b/docs/faq.rst @@ -192,6 +192,9 @@ compute nodes are isolated, or in PC/laptop enviroments if you are travelling. query for a template resource that has not been previously accessed. If you know what are the templates you are planning to use, you could prefetch them using the Python client. +In addition to the output-spaces that you specify, fmriprep will use +'MNI152NLin2009cAsym', 'MNI152NLin6Asym' and 'OASIS30ANTs' templates, that +also need to be prefetched. To do so, follow the next steps. 1. By default, a mirror of *TemplateFlow* to store the resources will be From 6dfe06bc5a5bf312efd063af42e6f153d6d34b77 Mon Sep 17 00:00:00 2001 From: basile Date: Mon, 22 Jun 2020 13:25:16 -0400 Subject: [PATCH 2/6] specify internal templates depending on execution options --- docs/faq.rst | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/faq.rst b/docs/faq.rst index bc4ef6d25..074d540b5 100644 --- a/docs/faq.rst +++ b/docs/faq.rst @@ -193,8 +193,9 @@ query for a template resource that has not been previously accessed. If you know what are the templates you are planning to use, you could prefetch them using the Python client. In addition to the output-spaces that you specify, fmriprep will use -'MNI152NLin2009cAsym', 'MNI152NLin6Asym' and 'OASIS30ANTs' templates, that -also need to be prefetched. +'MNI152NLin2009cAsym' and 'OASIS30ANTs' templates, +(as well as 'MNI152NLin6Asym' if `--cifti-output` or `--use-aroma` is specified), +that also need to be prefetched. To do so, follow the next steps. 1. By default, a mirror of *TemplateFlow* to store the resources will be From 5ae805f8ceb35c0ce9dab2a4b3e2b7175701fe63 Mon Sep 17 00:00:00 2001 From: basile Date: Tue, 23 Jun 2020 19:07:32 -0400 Subject: [PATCH 3/6] reformatting --- docs/faq.rst | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/faq.rst b/docs/faq.rst index 074d540b5..68f405a42 100644 --- a/docs/faq.rst +++ b/docs/faq.rst @@ -192,9 +192,9 @@ compute nodes are isolated, or in PC/laptop enviroments if you are travelling. query for a template resource that has not been previously accessed. If you know what are the templates you are planning to use, you could prefetch them using the Python client. -In addition to the output-spaces that you specify, fmriprep will use -'MNI152NLin2009cAsym' and 'OASIS30ANTs' templates, -(as well as 'MNI152NLin6Asym' if `--cifti-output` or `--use-aroma` is specified), +In addition to the output-spaces that you specify, *fMRIPrep* will use +``MNI152NLin2009cAsym`` and ``OASIS30ANTs`` templates, +(as well as ``MNI152NLin6Asym`` if ``--cifti-output`` or ``--use-aroma`` is specified), that also need to be prefetched. To do so, follow the next steps. From 4e7bc9dfa6fd7df39e14032674118918ce942106 Mon Sep 17 00:00:00 2001 From: Basile Date: Thu, 25 Jun 2020 09:11:16 -0400 Subject: [PATCH 4/6] Apply suggestions from code review Co-authored-by: Oscar Esteban --- docs/faq.rst | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/docs/faq.rst b/docs/faq.rst index 68f405a42..8bc2ceca3 100644 --- a/docs/faq.rst +++ b/docs/faq.rst @@ -192,9 +192,11 @@ compute nodes are isolated, or in PC/laptop enviroments if you are travelling. query for a template resource that has not been previously accessed. If you know what are the templates you are planning to use, you could prefetch them using the Python client. -In addition to the output-spaces that you specify, *fMRIPrep* will use -``MNI152NLin2009cAsym`` and ``OASIS30ANTs`` templates, -(as well as ``MNI152NLin6Asym`` if ``--cifti-output`` or ``--use-aroma`` is specified), +In addition to the ``--output-spaces`` that you specify, *fMRIPrep* will +internally require the ``MNI152NLin2009cAsym`` template. +If the ``--skull-strip-template`` option is not set, then ``OASIS30ANTs`` +will be used. +Finally, either ``--cifti-output`` or ``--use-aroma`` arguments require ``MNI152NLin6Asym``, that also need to be prefetched. To do so, follow the next steps. From b6015f6ea014c19ce73df8d0eccd4647f0c24150 Mon Sep 17 00:00:00 2001 From: basile Date: Thu, 25 Jun 2020 21:19:00 -0400 Subject: [PATCH 5/6] fix typos --- docs/faq.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/faq.rst b/docs/faq.rst index 68f405a42..efc988e29 100644 --- a/docs/faq.rst +++ b/docs/faq.rst @@ -187,7 +187,7 @@ How do you use TemplateFlow in the absence of access to the Internet? --------------------------------------------------------------------- This is a fairly common situation in :abbr:`HPCs (high-performance computing)` systems, where the so-called login nodes have access to the Internet but -compute nodes are isolated, or in PC/laptop enviroments if you are travelling. +compute nodes are isolated, or in PC/laptop environments if you are traveling. *TemplateFlow* will require Internet access the first time it receives a query for a template resource that has not been previously accessed. If you know what are the templates you are planning to use, you could From 824503168ebf6b000389160a7846311d0c7d7ac8 Mon Sep 17 00:00:00 2001 From: Basile Date: Thu, 2 Jul 2020 10:59:30 -0400 Subject: [PATCH 6/6] Update docs/faq.rst Co-authored-by: Mathias Goncalves --- docs/faq.rst | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/faq.rst b/docs/faq.rst index e17103b8c..49933c54c 100644 --- a/docs/faq.rst +++ b/docs/faq.rst @@ -196,8 +196,7 @@ In addition to the ``--output-spaces`` that you specify, *fMRIPrep* will internally require the ``MNI152NLin2009cAsym`` template. If the ``--skull-strip-template`` option is not set, then ``OASIS30ANTs`` will be used. -Finally, either ``--cifti-output`` or ``--use-aroma`` arguments require ``MNI152NLin6Asym``, -that also need to be prefetched. +Finally, both the ``--cifti-output`` and ``--use-aroma`` arguments require ``MNI152NLin6Asym``. To do so, follow the next steps. 1. By default, a mirror of *TemplateFlow* to store the resources will be