From 4eb5443948ff908437e3bda958ee0ea3bc8afb99 Mon Sep 17 00:00:00 2001 From: Jeff Mentch Date: Wed, 9 Dec 2020 13:35:10 -0500 Subject: [PATCH 1/8] update docs, skull stripping is forced by default docs say that the heuristic is used by default but at the moment skull stripping is forced #2318, updated docs to mention this --- docs/workflows.rst | 13 +++++-------- 1 file changed, 5 insertions(+), 8 deletions(-) diff --git a/docs/workflows.rst b/docs/workflows.rst index 4d2c19ff6..fde29db37 100644 --- a/docs/workflows.rst +++ b/docs/workflows.rst @@ -60,15 +60,12 @@ single reference template (see `Longitudinal processing`_). as if they are unprocessed. In the case of brain-extracted (skull-stripped) T1w images, attempting to perform brain extraction again will often have poor results and may cause *fMRIPrep* to crash. - By default, *fMRIPrep* will attempt to detect these cases using a heuristic to check if the - T1w image is already masked. + *fMRIPrep* can attempt to detect these cases using a heuristic to check if the + T1w image is already masked. This may be explicitly requested with + ``---skull-strip-t1w auto``. If this heuristic fails, and you know your images are skull-stripped, you can skip brain - extraction with ``--skull-strip-t1w skip``. - Likewise, if you know your images are not skull-stripped and the heuristic incorrectly - determines that they are, you can force skull stripping with ``--skull-strip-t1w force``. - The default behavior of detecting pre-extracted brains may be explicitly requested with - ``---skull-strip-t1w auto``, which will use a heuristic to check if each image is - already masked. + extraction with ``--skull-strip-t1w skip``. Likewise, if you know your images are not skull-stripped and the heuristic incorrectly + determines that they are, you can force skull stripping with ``--skull-strip-t1w force`` which is the current default behavior. See also *sMRIPrep*'s :py:func:`~smriprep.workflows.anatomical.init_anat_preproc_wf`. From 415aa9b8b205bf5a553ef636fc45464bd79536e6 Mon Sep 17 00:00:00 2001 From: Jeff Mentch Date: Wed, 9 Dec 2020 14:34:55 -0500 Subject: [PATCH 2/8] Update .zenodo.json --- .zenodo.json | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.zenodo.json b/.zenodo.json index 216eefe28..84c9255b8 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -2,6 +2,12 @@ "title": "fMRIPrep: a robust preprocessing pipeline for functional MRI", "description": "

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

", "contributors": [ + { + "affiliation": "Speech & Hearing Bioscience & Technology Program, Harvard University", + "name": "Mentch, Jeff", + "orcid": "0000-0002-7762-8678", + "type": "Researcher" + }, { "affiliation": "Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toru\u0144", "name": "Finc, Karolina", From c3bd4432c84f3bdea20cc9dccf152f00abee38b8 Mon Sep 17 00:00:00 2001 From: Jeff Mentch Date: Wed, 9 Dec 2020 14:37:08 -0500 Subject: [PATCH 3/8] Update docs/workflows.rst Co-authored-by: Mathias Goncalves --- docs/workflows.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/workflows.rst b/docs/workflows.rst index fde29db37..31cb7bd96 100644 --- a/docs/workflows.rst +++ b/docs/workflows.rst @@ -61,7 +61,7 @@ single reference template (see `Longitudinal processing`_). In the case of brain-extracted (skull-stripped) T1w images, attempting to perform brain extraction again will often have poor results and may cause *fMRIPrep* to crash. *fMRIPrep* can attempt to detect these cases using a heuristic to check if the - T1w image is already masked. This may be explicitly requested with + T1w image is already masked. This must be explicitly requested with ``---skull-strip-t1w auto``. If this heuristic fails, and you know your images are skull-stripped, you can skip brain extraction with ``--skull-strip-t1w skip``. Likewise, if you know your images are not skull-stripped and the heuristic incorrectly From f0b3e43bda0dca471e517dfece7b8dffbf92a5e2 Mon Sep 17 00:00:00 2001 From: Jeff Mentch Date: Wed, 9 Dec 2020 15:42:14 -0500 Subject: [PATCH 4/8] undo update to .zenodo.json --- .zenodo.json | 6 ------ 1 file changed, 6 deletions(-) diff --git a/.zenodo.json b/.zenodo.json index 84c9255b8..216eefe28 100644 --- a/.zenodo.json +++ b/.zenodo.json @@ -2,12 +2,6 @@ "title": "fMRIPrep: a robust preprocessing pipeline for functional MRI", "description": "

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.

", "contributors": [ - { - "affiliation": "Speech & Hearing Bioscience & Technology Program, Harvard University", - "name": "Mentch, Jeff", - "orcid": "0000-0002-7762-8678", - "type": "Researcher" - }, { "affiliation": "Centre for Modern Interdisciplinary Technologies, Nicolaus Copernicus University in Toru\u0144", "name": "Finc, Karolina", From 1656740e3abe4a7fa31e5c7a26aaa17cdf475f9e Mon Sep 17 00:00:00 2001 From: Jeff Mentch Date: Wed, 9 Dec 2020 15:43:55 -0500 Subject: [PATCH 5/8] update contributors --- .maint/contributors.json | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/.maint/contributors.json b/.maint/contributors.json index c599f2461..6ba2246a3 100644 --- a/.maint/contributors.json +++ b/.maint/contributors.json @@ -114,6 +114,12 @@ "name": "Ma, Feilong", "orcid": "0000-0002-6838-3971" }, + { + "affiliation": "Speech & Hearing Bioscience & Technology Program, Harvard University", + "name": "Mentch, Jeff", + "orcid": "0000-0002-7762-8678", + "type": "Researcher" + }, { "affiliation": "Department of Psychology, Stanford University", "name": "Moodie, Craig A.", From e0fd7ddcd2ddada3c626b54ce1eba6bd681b1503 Mon Sep 17 00:00:00 2001 From: Jeff Mentch Date: Wed, 9 Dec 2020 15:48:36 -0500 Subject: [PATCH 6/8] fix linebreaks docs/workflows.rst fix linebreaks Co-authored-by: Chris Markiewicz --- docs/workflows.rst | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/docs/workflows.rst b/docs/workflows.rst index 31cb7bd96..f1e72dd42 100644 --- a/docs/workflows.rst +++ b/docs/workflows.rst @@ -61,8 +61,8 @@ single reference template (see `Longitudinal processing`_). In the case of brain-extracted (skull-stripped) T1w images, attempting to perform brain extraction again will often have poor results and may cause *fMRIPrep* to crash. *fMRIPrep* can attempt to detect these cases using a heuristic to check if the - T1w image is already masked. This must be explicitly requested with - ``---skull-strip-t1w auto``. + T1w image is already masked. + This must be explicitly requested with ``---skull-strip-t1w auto``. If this heuristic fails, and you know your images are skull-stripped, you can skip brain extraction with ``--skull-strip-t1w skip``. Likewise, if you know your images are not skull-stripped and the heuristic incorrectly determines that they are, you can force skull stripping with ``--skull-strip-t1w force`` which is the current default behavior. From 6a02ab323d7deae31f23d923a09d0af21d9c9980 Mon Sep 17 00:00:00 2001 From: Jeff Mentch Date: Wed, 9 Dec 2020 15:49:47 -0500 Subject: [PATCH 7/8] Update docs/workflows.rst fix wording Co-authored-by: Oscar Esteban --- docs/workflows.rst | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/docs/workflows.rst b/docs/workflows.rst index f1e72dd42..79f993d51 100644 --- a/docs/workflows.rst +++ b/docs/workflows.rst @@ -64,8 +64,10 @@ single reference template (see `Longitudinal processing`_). T1w image is already masked. This must be explicitly requested with ``---skull-strip-t1w auto``. If this heuristic fails, and you know your images are skull-stripped, you can skip brain - extraction with ``--skull-strip-t1w skip``. Likewise, if you know your images are not skull-stripped and the heuristic incorrectly - determines that they are, you can force skull stripping with ``--skull-strip-t1w force`` which is the current default behavior. + extraction with ``--skull-strip-t1w skip``. + Likewise, if you know your images are not skull-stripped and the heuristic incorrectly + determines that they are, you can force skull stripping with ``--skull-strip-t1w force``, + which is the current default behavior. See also *sMRIPrep*'s :py:func:`~smriprep.workflows.anatomical.init_anat_preproc_wf`. From f74cd6ba368512dee96c07f60b3df3c4929c43e4 Mon Sep 17 00:00:00 2001 From: Jeff Mentch Date: Wed, 9 Dec 2020 16:06:59 -0500 Subject: [PATCH 8/8] fix spacing, indent --- docs/workflows.rst | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/workflows.rst b/docs/workflows.rst index 79f993d51..08b7b4f1d 100644 --- a/docs/workflows.rst +++ b/docs/workflows.rst @@ -67,7 +67,7 @@ single reference template (see `Longitudinal processing`_). extraction with ``--skull-strip-t1w skip``. Likewise, if you know your images are not skull-stripped and the heuristic incorrectly determines that they are, you can force skull stripping with ``--skull-strip-t1w force``, - which is the current default behavior. + which is the current default behavior. See also *sMRIPrep*'s :py:func:`~smriprep.workflows.anatomical.init_anat_preproc_wf`.