From fb5f567ae11054cef48c71435e5d4850814acacf Mon Sep 17 00:00:00 2001 From: Marcel Zwiers Date: Wed, 22 Jun 2022 12:15:15 +0200 Subject: [PATCH] Update ciftify_clean_img.py If confounds are not given then an error occurs. The PR is a minimal patch for this Traceback (most recent call last): File "/home/mrphys/marzwi/.conda/envs/ciftify/bin/ciftify_clean_img", line 8, in sys.exit(main()) File "/home/mrphys/marzwi/.conda/envs/ciftify/lib/python3.9/site-packages/ciftify/bin/ciftify_clean_img.py", line 376, in main ret = run_ciftify_clean_img(arguments, tmpdir) File "/home/mrphys/marzwi/.conda/envs/ciftify/lib/python3.9/site-packages/ciftify/bin/ciftify_clean_img.py", line 254, in run_ciftify_clean_img clean_output = clean_image_with_nilearn(trimmed_nifti, confound_signals, settings) File "/home/mrphys/marzwi/.conda/envs/ciftify/lib/python3.9/site-packages/ciftify/bin/ciftify_clean_img.py", line 345, in clean_image_with_nilearn confounds=confound_signals.values, AttributeError: 'NoneType' object has no attribute 'values' --- ciftify/bin/ciftify_clean_img.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/ciftify/bin/ciftify_clean_img.py b/ciftify/bin/ciftify_clean_img.py index eac595f..60f9f0e 100755 --- a/ciftify/bin/ciftify_clean_img.py +++ b/ciftify/bin/ciftify_clean_img.py @@ -342,7 +342,7 @@ def clean_image_with_nilearn(input_img, confound_signals, settings): clean_output = nilearn.image.clean_img(input_img, detrend=settings.detrend, standardize=settings.standardize, - confounds=confound_signals.values, + confounds=confound_signals.values if confound_signals is not None else None, low_pass=settings.low_pass, high_pass=settings.high_pass, t_r=settings.func.tr)