diff --git a/tedana/tests/test_t2smap.py b/tedana/tests/test_t2smap.py index e52f24dfd..2dddc5754 100644 --- a/tedana/tests/test_t2smap.py +++ b/tedana/tests/test_t2smap.py @@ -27,13 +27,13 @@ def test_basic_t2smap1(self): # Check outputs assert op.isfile(op.join(out_dir, 'desc-optcom_bold.nii.gz')) - img = nib.load(op.join(out_dir, 'T2StarMap.nii.gz')) + img = nib.load(op.join(out_dir, 'T2starmap.nii.gz')) assert len(img.shape) == 3 - img = nib.load(op.join(out_dir, 'S0Map.nii.gz')) + img = nib.load(op.join(out_dir, 'S0map.nii.gz')) assert len(img.shape) == 3 - img = nib.load(op.join(out_dir, 'desc-full_T2StarMap.nii.gz')) + img = nib.load(op.join(out_dir, 'desc-full_T2starmap.nii.gz')) assert len(img.shape) == 3 - img = nib.load(op.join(out_dir, 'desc-full_S0Map.nii.gz')) + img = nib.load(op.join(out_dir, 'desc-full_S0map.nii.gz')) assert len(img.shape) == 3 img = nib.load(op.join(out_dir, 'desc-optcom_bold.nii.gz')) assert len(img.shape) == 4 @@ -53,13 +53,13 @@ def test_basic_t2smap2(self): # Check outputs assert op.isfile(op.join(out_dir, 'desc-optcom_bold.nii.gz')) - img = nib.load(op.join(out_dir, 'T2StarMap.nii.gz')) + img = nib.load(op.join(out_dir, 'T2starmap.nii.gz')) assert len(img.shape) == 4 - img = nib.load(op.join(out_dir, 'S0Map.nii.gz')) + img = nib.load(op.join(out_dir, 'S0map.nii.gz')) assert len(img.shape) == 4 - img = nib.load(op.join(out_dir, 'desc-full_T2StarMap.nii.gz')) + img = nib.load(op.join(out_dir, 'desc-full_T2starmap.nii.gz')) assert len(img.shape) == 4 - img = nib.load(op.join(out_dir, 'desc-full_S0Map.nii.gz')) + img = nib.load(op.join(out_dir, 'desc-full_S0map.nii.gz')) assert len(img.shape) == 4 img = nib.load(op.join(out_dir, 'desc-optcom_bold.nii.gz')) assert len(img.shape) == 4 @@ -79,13 +79,13 @@ def test_basic_t2smap3(self): # Check outputs assert op.isfile(op.join(out_dir, 'desc-optcom_bold.nii.gz')) - img = nib.load(op.join(out_dir, 'T2StarMap.nii.gz')) + img = nib.load(op.join(out_dir, 'T2starmap.nii.gz')) assert len(img.shape) == 3 - img = nib.load(op.join(out_dir, 'S0Map.nii.gz')) + img = nib.load(op.join(out_dir, 'S0map.nii.gz')) assert len(img.shape) == 3 - img = nib.load(op.join(out_dir, 'desc-full_T2StarMap.nii.gz')) + img = nib.load(op.join(out_dir, 'desc-full_T2starmap.nii.gz')) assert len(img.shape) == 3 - img = nib.load(op.join(out_dir, 'desc-full_S0Map.nii.gz')) + img = nib.load(op.join(out_dir, 'desc-full_S0map.nii.gz')) assert len(img.shape) == 3 img = nib.load(op.join(out_dir, 'desc-optcom_bold.nii.gz')) assert len(img.shape) == 4 @@ -105,13 +105,13 @@ def test_basic_t2smap4(self): # Check outputs assert op.isfile(op.join(out_dir, 'desc-optcom_bold.nii.gz')) - img = nib.load(op.join(out_dir, 'T2StarMap.nii.gz')) + img = nib.load(op.join(out_dir, 'T2starmap.nii.gz')) assert len(img.shape) == 4 - img = nib.load(op.join(out_dir, 'S0Map.nii.gz')) + img = nib.load(op.join(out_dir, 'S0map.nii.gz')) assert len(img.shape) == 4 - img = nib.load(op.join(out_dir, 'desc-full_T2StarMap.nii.gz')) + img = nib.load(op.join(out_dir, 'desc-full_T2starmap.nii.gz')) assert len(img.shape) == 4 - img = nib.load(op.join(out_dir, 'desc-full_S0Map.nii.gz')) + img = nib.load(op.join(out_dir, 'desc-full_S0map.nii.gz')) assert len(img.shape) == 4 img = nib.load(op.join(out_dir, 'desc-optcom_bold.nii.gz')) assert len(img.shape) == 4 @@ -131,13 +131,13 @@ def test_t2smap_cli(self): workflows.t2smap._main(args) # Check outputs - img = nib.load(op.join(out_dir, 'T2StarMap.nii.gz')) + img = nib.load(op.join(out_dir, 'T2starmap.nii.gz')) assert len(img.shape) == 3 - img = nib.load(op.join(out_dir, 'S0Map.nii.gz')) + img = nib.load(op.join(out_dir, 'S0map.nii.gz')) assert len(img.shape) == 3 - img = nib.load(op.join(out_dir, 'desc-full_T2StarMap.nii.gz')) + img = nib.load(op.join(out_dir, 'desc-full_T2starmap.nii.gz')) assert len(img.shape) == 3 - img = nib.load(op.join(out_dir, 'desc-full_S0Map.nii.gz')) + img = nib.load(op.join(out_dir, 'desc-full_S0map.nii.gz')) assert len(img.shape) == 3 img = nib.load(op.join(out_dir, 'desc-optcom_bold.nii.gz')) assert len(img.shape) == 4 diff --git a/tedana/workflows/t2smap.py b/tedana/workflows/t2smap.py index ac5a66b8b..85ab44d3d 100644 --- a/tedana/workflows/t2smap.py +++ b/tedana/workflows/t2smap.py @@ -152,7 +152,7 @@ def t2smap_workflow(data, tes, out_dir='.', mask=None, debug : :obj:`bool`, optional Whether to run in debugging mode or not. Default is False. quiet : :obj:`bool`, optional - If True, suppresses logging/printing of messages. Default is False. + If True, suppress logging/printing of messages. Default is False. Notes @@ -162,16 +162,16 @@ def t2smap_workflow(data, tes, out_dir='.', mask=None, ========================== ================================================= Filename Content ========================== ================================================= - T2StarMap.nii.gz Limited estimated T2* 3D map or 4D timeseries. + T2starmap.nii.gz Limited estimated T2* 3D map or 4D timeseries. Will be a 3D map if ``fitmode`` is 'all' and a 4D timeseries if it is 'ts'. - S0Map.nii.gz Limited S0 3D map or 4D timeseries. - desc-full_T2StarMap.nii.gz Full T2* map/timeseries. The difference between + S0map.nii.gz Limited S0 3D map or 4D timeseries. + desc-full_T2starmap.nii.gz Full T2* map/timeseries. The difference between the limited and full maps is that, for voxels affected by dropout where only one echo contains good data, the full map uses the single echo's value while the limited map has a NaN. - desc-full_S0Map.nii.gz Full S0 map/timeseries. + desc-full_S0map.nii.gz Full S0 map/timeseries. desc-optcom_bold.nii.gz Optimally combined timeseries. ========================== ================================================= """ @@ -238,11 +238,11 @@ def t2smap_workflow(data, tes, out_dir='.', mask=None, t2s_limited[t2s_limited < 0] = 0 io.filewrite(utils.millisec2sec(t2s_limited), - op.join(out_dir, 'T2StarMap.nii.gz'), ref_img) - io.filewrite(s0_limited, op.join(out_dir, 'S0Map.nii.gz'), ref_img) + op.join(out_dir, 'T2starmap.nii.gz'), ref_img) + io.filewrite(s0_limited, op.join(out_dir, 'S0map.nii.gz'), ref_img) io.filewrite(utils.millisec2sec(t2s_full), - op.join(out_dir, 'desc-full_T2StarMap.nii.gz'), ref_img) - io.filewrite(s0_full, op.join(out_dir, 'desc-full_S0Map.nii.gz'), ref_img) + op.join(out_dir, 'desc-full_T2starmap.nii.gz'), ref_img) + io.filewrite(s0_full, op.join(out_dir, 'desc-full_S0map.nii.gz'), ref_img) io.filewrite(OCcatd, op.join(out_dir, 'desc-optcom_bold.nii.gz'), ref_img)