remove gunzip

nipype · djarecka · Oct 7, 2022 · Jul 27, 2022 · Jul 27, 2022 · Jul 27, 2022
commit e047b620bcc13066435ce58fa3832fabb586206b
diff --git a/notebooks/7_twolevel_glm_nilearn.md b/notebooks/7_twolevel_glm_nilearn.md
@@ -244,12 +244,9 @@ def firstlevel_estimation(subj_id, subj_imgs, subj_masks, smoothing_fwhm, design
     mask = math_img('img > 0', img=mean_mask)
     print('Fit the firstlevel model...')
     # fit the (fixed-effects) firstlevel model with three runs simultaneously
-    first_level_model = FirstLevelModel(mask_img=mask, smoothing_fwhm=smoothing_fwhm)
+    first_level_model = FirstLevelModel(mask_img=mask, smoothing_fwhm=smoothing_fwhm, n_job=-1)
     dms = [pd.read_csv(pth) for pth in design_matrices]
-    for img in subj_imgs:
-        gunzip(img)
-    subj_imgs_unzip = [img.split('.gz')[0] for img in subj_imgs]
-    first_level_model = first_level_model.fit(subj_imgs_unzip, design_matrices=dms)
+    first_level_model = first_level_model.fit(subj_imgs, design_matrices=dms)
     print('Computing contrasts...')
     z_map_path_dict = dict.fromkeys(contrasts.keys())
     for index, (contrast_id, contrast_val) in enumerate(contrasts.items()):
@@ -269,6 +266,11 @@ def firstlevel_estimation(subj_id, subj_imgs, subj_masks, smoothing_fwhm, design
 ### Create the first-level GLM workflow
 
 ```{code-cell} ipython3
+---
+jupyter:
+  outputs_hidden: true
+tags: []
+---
 # initiate the first-level GLM workflow
 wf_firstlevel = Workflow(
     name='wf_firstlevel',