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arielletambini / denoiser

Nuisance removal tool for fMRI data
Apache License 2.0
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Problem running denoise #35

Open manzouri opened 3 years ago

manzouri commented 3 years ago

Hi, I am trying to run denoise on my data but getting the following error: Command: 'python run_denoise.py /home/data/OUT/derivatives/fmriprep/sub-101/ses-01/func/sub-101_ses-01_task-touch_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz /home/data/OUT/derivatives/fmriprep/sub-101/ses-01/func/sub-101_ses-01_task-touch_run-1_desc-confounds_timeseries.tsv /home/data/OUT/derivatives/fmriprep/sub-101/ses-01/func/ --col_names csf white_matter framewise_displacement --hp_filter 0.01'

Output: /home/amiman/anaconda3/lib/python3.7/site-packages/nilearn/glm/init.py:56: FutureWarning: The nilearn.glm module is experimental. It may change in any future release of Nilearn. 'It may change in any future release of Nilearn.', FutureWarning) /home/amiman/anaconda3/lib/python3.7/site-packages/sklearn/feature_extraction/text.py:17: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated, and in 3.8 it will stop working from collections import Mapping, defaultdict

of TRs: 296

Filling in 1 NaN value for framewise_displacement

of Confound Regressors: 3 [SELECTED regressors in CSV]

of High-pass Filter Regressors: 9

Saving output file... Output directory: /home/data/OUT/derivatives/fmriprep/sub-101/ses-01/func/sub-101_ses-01_task-touch_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold_NR_figures FD not found: FD timeseries not plotted Computing dvars... Traceback (most recent call last): File "run_denoise.py", line 463, in denoise(img_file, tsv_file, out_path, col_names, hp_filter, lp_filter, out_figure_path) File "run_denoise.py", line 376, in denoise del fig, ax0, ax_curr, ax_d, dvars UnboundLocalError: local variable 'ax0' referenced before assignment

arielletambini commented 3 years ago

I also obtained a similar error (due to the 'framewise_displacement' field not being listed as an option for the FD column name), and modified the code yesterday to fix this. Could you pull the updated version and see if this fixes the error? Alternatively, what is the name of the framewise displacement column in the .tsv file that you are using?

manzouri commented 3 years ago

Hi and thanks . I will try it . The name is "framewise_displacement" in the .tsv file.

manzouri commented 3 years ago

Hi again, Now it runs without error and I get the output file but not the output html. IS there anything I missed?