diff --git a/content/00_Download_Data.md b/content/00_Download_Data.md index 12dab6c1..124dcf3c 100644 --- a/content/00_Download_Data.md +++ b/content/00_Download_Data.md @@ -23,4 +23,6 @@ cd ../data/ds006185 datalad get -J5 sub-24053/ses-1/func/sub-24053_ses-1_task-rat_dir-PA_run-01_echo-* datalad get sub-24053/ses-1/func/sub-24053_ses-1_task-rat_dir-PA_run-01_part-mag_desc-brain_mask.nii.gz datalad get sub-24053/ses-1/func/sub-24053_ses-1_task-rat_dir-PA_run-01_part-mag_desc-confounds_timeseries.tsv +datalad get sub-24053/ses-1/func/sub-24053_ses-1_task-rat_dir-PA_run-01_from-boldref_to-T1w_mode-image_desc-coreg_xfm.txt +datalad get sub-24053/ses-1/anat/sub-24053_ses-1_rec-norm_desc-preproc_T1w.nii.gz ``` diff --git a/content/plot_approach_figures.md b/content/plot_approach_figures.md index fe0c3434..33cc150d 100644 --- a/content/plot_approach_figures.md +++ b/content/plot_approach_figures.md @@ -35,6 +35,7 @@ from tedana.utils import make_adaptive_mask data_path = os.path.abspath('../data') +func_dir = os.path.join(data_path, "ds006185/sub-24053/ses-1/func/") ted_dir = os.path.join(data_path, "tedana") ``` @@ -42,6 +43,9 @@ ted_dir = os.path.join(data_path, "tedana") ```{code-cell} ipython3 :tags: [hide-cell] data = load_pafin(data_path) +# load_pafin returns echo_times as a list; this chapter does array arithmetic on +# it (e.g. -1 * echo_times), so coerce to an array once here. +data['echo_times'] = np.asarray(data['echo_times']) # Background anatomical image anat_dir = os.path.join(data_path, "ds006185/sub-24053/ses-1/anat/")