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Merged
merged 21 commits into from
May 13, 2020
+21 −18
Merged

[MAINT] Pin tedana version #2117

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cfab513
Update tedana version.
tsalo Apr 1, 2020
e2bdeba
Remove full T2*/S0 maps from T2SMapOutputSpec.
tsalo Apr 1, 2020
7505b34
Change T2SMapOutputSpec filenames.
tsalo Apr 1, 2020
9691541
Make curvefit default for T2*/S0 estimation.
tsalo Apr 1, 2020
191b240
Merge remote-tracking branch 'poldracklab/master' into maint/tedana-v…
tsalo Apr 1, 2020
5c3aa20
Drop TED directory and use default output directory (CWD).
tsalo Apr 2, 2020
ce34324
Merge remote-tracking branch 'poldracklab/master' into maint/tedana-v…
tsalo Apr 25, 2020
d95928f
Fix t2smap output names.
tsalo Apr 28, 2020
09fc5ea
Merge remote-tracking branch 'poldracklab/master' into maint/tedana-v…
tsalo Apr 28, 2020
379f0bd
Update T2* workflow report to match new changes.
tsalo Apr 29, 2020
20f480c
Merge remote-tracking branch 'poldracklab/master' into maint/tedana-v…
tsalo May 5, 2020
b07a78e
Remove unused imports.
tsalo May 5, 2020
8f4a7a9
Change pinned version to alpha.
tsalo May 5, 2020
444d6b8
Fix T2* workflow subsection title.
tsalo May 5, 2020
84be38d
Hopefully fix output file paths.
tsalo May 5, 2020
d80d164
Fix getcwd().
tsalo May 5, 2020
0d38986
Fix fittype argument.
tsalo May 5, 2020
2d040d8
Update tedana version for bug-fix.
tsalo May 10, 2020
4a63f8b
Merge remote-tracking branch 'poldracklab/master' into maint/tedana-v…
tsalo May 10, 2020
0183a4b
Apply suggestions from @mgxd's review
tsalo May 12, 2020
ff132a5
Grab most recent version in 0.0.9 series.
tsalo May 12, 2020
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4 changes: 2 additions & 2 deletions docs/workflows.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -568,8 +568,8 @@ A visualization of the AROMA component classification is also included in the HT

.. _bold_t2s:

T2* Driven Coregistration
~~~~~~~~~~~~~~~~~~~~~~~~~
T2*-driven echo combination
~~~~~~~~~~~~~~~~~~~~~~~~~~~
:py:func:`~fmriprep.workflows.bold.t2s.init_bold_t2s_wf`

If multi-echo :abbr:`BOLD (blood-oxygen level-dependent)` data is supplied,
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33 changes: 18 additions & 15 deletions fmriprep/interfaces/multiecho.py
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Expand Up @@ -15,8 +15,7 @@
>>> os.chdir(datadir)

"""
import os
from nibabel.filename_parser import splitext_addext
import os.path

from nipype import logging
from nipype.interfaces.base import (
Expand All @@ -39,13 +38,22 @@ class T2SMapInputSpec(CommandLineInputSpec):
mandatory=True,
minlen=3,
desc='echo times')
fittype = traits.Enum('curvefit', 'loglin',
argstr='--fittype %s',
position=3,
mandatory=False,
usedefault=True,
desc=('Desired fitting method: '
'"loglin" means that a linear model is fit '
'to the log of the data. '
'"curvefit" means that a more computationally '
'demanding monoexponential model is fit '
'to the raw data.'))


class T2SMapOutputSpec(TraitedSpec):
t2star_map = File(exists=True, desc='limited T2* map')
s0_map = File(exists=True, desc='limited s0 map')
t2star_adaptive_map = File(exists=True, desc='adaptive T2* map')
s0_adaptive_map = File(exists=True, desc='adaptive s0 map')
s0_map = File(exists=True, desc='limited S0 map')
optimal_comb = File(exists=True, desc='optimally combined ME-EPI time series')


Expand All @@ -64,7 +72,7 @@ class T2SMap(CommandLine):
>>> t2smap.inputs.echo_times = [0.013, 0.027, 0.043]
>>> t2smap.cmdline # doctest: +ELLIPSIS
't2smap -d sub-01_run-01_echo-1_bold.nii.gz sub-01_run-01_echo-2_bold.nii.gz \
sub-01_run-01_echo-3_bold.nii.gz -e 13.0 27.0 43.0'
sub-01_run-01_echo-3_bold.nii.gz -e 13.0 27.0 43.0 --fittype curvefit'
"""
_cmd = 't2smap'
input_spec = T2SMapInputSpec
Expand All @@ -77,13 +85,8 @@ def _format_arg(self, name, trait_spec, value):

def _list_outputs(self):
outputs = self._outputs().get()
filename = splitext_addext(os.path.basename(self.inputs.in_files[0]))[0]
out_dir = os.path.abspath('TED.{}'.format(filename))

outputs['t2star_map'] = os.path.join(out_dir, 't2sv.nii')
outputs['s0_map'] = os.path.join(out_dir, 's0v.nii')
outputs['t2star_adaptive_map'] = os.path.join(out_dir, 't2svG.nii')
outputs['s0_adaptive_map'] = os.path.join(out_dir, 's0vG.nii')
outputs['optimal_comb'] = os.path.join(out_dir, 'ts_OC.nii')

out_dir = os.getcwd()
outputs['t2star_map'] = os.path.join(out_dir, 'T2starmap.nii.gz')
outputs['s0_map'] = os.path.join(out_dir, 'S0map.nii.gz')
outputs['optimal_comb'] = os.path.join(out_dir, 'desc-optcom_bold.nii.gz')
return outputs
3 changes: 2 additions & 1 deletion fmriprep/workflows/bold/t2s.py
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Expand Up @@ -61,7 +61,8 @@ def init_bold_t2s_wf(echo_times, mem_gb, omp_nthreads,
workflow = Workflow(name=name)
workflow.__desc__ = """\
A T2* map was estimated from the preprocessed BOLD by fitting to a monoexponential signal
decay model with log-linear regression.
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
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2 changes: 1 addition & 1 deletion setup.cfg
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Expand Up @@ -35,7 +35,7 @@ install_requires =
pyyaml
sdcflows @ git+https://github.com/nipreps/sdcflows.git@master
smriprep @ git+https://github.com/poldracklab/smriprep.git@master
tedana >= 0.0.5
tedana ~= 0.0.9a1
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@mgxd mgxd May 12, 2020

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will this pick up 0.0.9? When pinning RCs in the past, we've had to do this manually, i.e.
>= 0.0.9a1, < 0.0.10

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@tsalo tsalo May 12, 2020

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It was able to grab 0.0.9a1 in the tests, but I wasn't thinking about 0.0.9. Should I switch to >= 0.0.9a1, < 0.0.10 so it grabs 0.0.9 once it's released, or is it okay to pin to 0.0.9a1?

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@mgxd mgxd May 12, 2020

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i would lean towards allowing grabbing a more stable version, but i'm not familiar with tedana's release cycle so whatever you think would be best

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@tsalo tsalo May 12, 2020

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That should be fine. I'm happy to change it.

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@mgxd mgxd May 12, 2020

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we can always increase/drop the maximum version, thanks!

templateflow ~= 0.6
toml
test_requires =
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