diff --git a/xcp_d/interfaces/execsummary.py b/xcp_d/interfaces/execsummary.py index 7dc6a6403..f5b2b6500 100644 --- a/xcp_d/interfaces/execsummary.py +++ b/xcp_d/interfaces/execsummary.py @@ -89,14 +89,14 @@ def collect_inputs(self): ANAT_REGISTRATION_DESCS = [ "AtlasOnAnat", "AnatOnAtlas", - "AtlasOnSubcorticals", - "SubcorticalsOnAtlas", + # "AtlasOnSubcorticals", + # "SubcorticalsOnAtlas", ] ANAT_REGISTRATION_TITLES = [ "Atlas On {modality}", # noqa: FS003 "{modality} On Atlas", # noqa: FS003 - "Atlas On {modality} Subcorticals", # noqa: FS003 - "{modality} Subcorticals On Atlas", # noqa: FS003 + # "Atlas On {modality} Subcorticals", # noqa: FS003 + # "{modality} Subcorticals On Atlas", # noqa: FS003 ] TASK_REGISTRATION_DESCS = [ "TaskOnT1w", diff --git a/xcp_d/interfaces/plotting.py b/xcp_d/interfaces/plotting.py index 92a43c4b9..97dc5ba2f 100644 --- a/xcp_d/interfaces/plotting.py +++ b/xcp_d/interfaces/plotting.py @@ -679,7 +679,15 @@ def _run_interface(self, runtime): arr = img.get_fdata() fig = plt.figure(constrained_layout=False, figsize=(25, 10)) - plot_anat(img, draw_cross=False, figure=fig, vmin=np.min(arr), vmax=np.max(arr)) + plot_anat( + img, + draw_cross=False, + figure=fig, + vmin=np.min(arr), + vmax=np.max(arr), + cut_coords=[0, 0, 0], + annotate=False, + ) fig.savefig(self._results["out_file"], bbox_inches="tight", pad_inches=None) plt.close(fig) diff --git a/xcp_d/utils/confounds.py b/xcp_d/utils/confounds.py index bc9223489..28f645488 100644 --- a/xcp_d/utils/confounds.py +++ b/xcp_d/utils/confounds.py @@ -73,15 +73,17 @@ def load_motion( ) # Volterra expansion - columns = motion_confounds_df.columns.tolist() - for col in columns: - new_col = f"{col}_derivative1" - motion_confounds_df[new_col] = motion_confounds_df[col].diff() - - columns = motion_confounds_df.columns.tolist() - for col in columns: - new_col = f"{col}_power2" - motion_confounds_df[new_col] = motion_confounds_df[col] ** 2 + # Ignore pandas SettingWithCopyWarning + with pd.option_context("mode.chained_assignment", None): + columns = motion_confounds_df.columns.tolist() + for col in columns: + new_col = f"{col}_derivative1" + motion_confounds_df[new_col] = motion_confounds_df[col].diff() + + columns = motion_confounds_df.columns.tolist() + for col in columns: + new_col = f"{col}_power2" + motion_confounds_df[new_col] = motion_confounds_df[col] ** 2 return motion_confounds_df