From 77b4cf250b11c397ef8e59f711989e9660a8527d Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Wed, 20 Oct 2021 09:55:10 +0200 Subject: [PATCH 1/4] DOC: ME | Add missing output to documentation, improve boilerplate --- fmriprep/workflows/bold/t2s.py | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/fmriprep/workflows/bold/t2s.py b/fmriprep/workflows/bold/t2s.py index 00a5b0dad..6f8b700c1 100644 --- a/fmriprep/workflows/bold/t2s.py +++ b/fmriprep/workflows/bold/t2s.py @@ -76,18 +76,20 @@ def init_bold_t2s_wf(echo_times, mem_gb, omp_nthreads, ------- bold the optimally combined time series for all supplied echos + t2star_map + the calculated T2:sup:`★` map """ from niworkflows.engine.workflows import LiterateWorkflow as Workflow workflow = Workflow(name=name) workflow.__desc__ = """\ -A T2\\* map was estimated from the preprocessed BOLD by fitting to a monoexponential signal -decay model with nonlinear regression, using T2\\*/S0 estimates from a log-linear -regression fit as initial values. -For each voxel, the maximal number of echoes with reliable signal in that voxel were -used to fit the model. -The calculated T2\\* map was then used to optimally combine preprocessed BOLD across +A T2★ map was estimated from the preprocessed EPI echoes, by voxel-wise fitting +the maximal number of echoes with reliable signal in that voxel to a monoexponential signal +decay model with nonlinear regression. +The T2★/S0 estimates from a log-linear regression fit were used for +initial values. +The calculated T2★ map was then used to optimally combine preprocessed BOLD across echoes following the method described in [@posse_t2s]. The optimally combined time series was carried forward as the *preprocessed BOLD*. """ From dfd99be3deb40f4a3263cd9e8310edf5add60e20 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Wed, 20 Oct 2021 10:11:02 +0200 Subject: [PATCH 2/4] Update t2s.py --- fmriprep/workflows/bold/t2s.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/fmriprep/workflows/bold/t2s.py b/fmriprep/workflows/bold/t2s.py index 6f8b700c1..ef1fbef1d 100644 --- a/fmriprep/workflows/bold/t2s.py +++ b/fmriprep/workflows/bold/t2s.py @@ -44,11 +44,11 @@ def init_bold_t2s_wf(echo_times, mem_gb, omp_nthreads, Combine multiple echos of :abbr:`ME-EPI (multi-echo echo-planar imaging)`. This workflow wraps the `tedana`_ `T2* workflow`_ to optimally - combine multiple echos and derive a T2* map. + combine multiple echos and derive a T2\ :sup:`★` map. The following steps are performed: #. :abbr:`HMC (head motion correction)` on individual echo files. - #. Compute the T2* map + #. Compute the T2\ :sup:`★` map #. Create an optimally combined ME-EPI time series .. _tedana: https://github.com/me-ica/tedana @@ -77,7 +77,7 @@ def init_bold_t2s_wf(echo_times, mem_gb, omp_nthreads, bold the optimally combined time series for all supplied echos t2star_map - the calculated T2:sup:`★` map + the calculated T2\ :sup:`★` map """ from niworkflows.engine.workflows import LiterateWorkflow as Workflow From 43070d6279f5ab442c413ca1c9688ca01de8be0c Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Wed, 20 Oct 2021 10:15:14 +0200 Subject: [PATCH 3/4] Update t2s.py --- fmriprep/workflows/bold/t2s.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fmriprep/workflows/bold/t2s.py b/fmriprep/workflows/bold/t2s.py index ef1fbef1d..ee2f126be 100644 --- a/fmriprep/workflows/bold/t2s.py +++ b/fmriprep/workflows/bold/t2s.py @@ -40,7 +40,7 @@ # pylint: disable=R0914 def init_bold_t2s_wf(echo_times, mem_gb, omp_nthreads, name='bold_t2s_wf'): - """ + r""" Combine multiple echos of :abbr:`ME-EPI (multi-echo echo-planar imaging)`. This workflow wraps the `tedana`_ `T2* workflow`_ to optimally From 8fbb02620d79334d592a1de1b7a281bfa654be81 Mon Sep 17 00:00:00 2001 From: Oscar Esteban Date: Wed, 20 Oct 2021 16:43:19 +0200 Subject: [PATCH 4/4] Apply suggestions from code review Co-authored-by: Taylor Salo --- fmriprep/workflows/bold/t2s.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/fmriprep/workflows/bold/t2s.py b/fmriprep/workflows/bold/t2s.py index ee2f126be..77d434a2e 100644 --- a/fmriprep/workflows/bold/t2s.py +++ b/fmriprep/workflows/bold/t2s.py @@ -44,10 +44,8 @@ def init_bold_t2s_wf(echo_times, mem_gb, omp_nthreads, Combine multiple echos of :abbr:`ME-EPI (multi-echo echo-planar imaging)`. This workflow wraps the `tedana`_ `T2* workflow`_ to optimally - combine multiple echos and derive a T2\ :sup:`★` map. + combine multiple preprocessed echos and derive a T2\ :sup:`★` map. The following steps are performed: - - #. :abbr:`HMC (head motion correction)` on individual echo files. #. Compute the T2\ :sup:`★` map #. Create an optimally combined ME-EPI time series