Nilearn Firstlevelmodel from BIDS unable to find bold images

Software Support
1

Hi all,

I am learning how to use Nilearn for MRI analysis, and I am running into the following error when trying to run a first-level GLM using first_level_from_bids:

ValueError: 2 events.tsv files found for 0 bold files. Same number of event files as the number of runs is expected

I have been following the User Guide: First level analysis of a complete BIDS dataset from openneuro - Nilearn

Here is my command:

from nilearn.glm.first_level import first_level_from_bids
data_dir = '/Volumes/Pegasus/nilearn/rawdata'
task_label = 'card'
space_label = 'MNI152NLin2009cAsym'
derivatives_folder = '/Volumes/Pegasus/nilearn/derivatives/fmriprep'
models, models_run_imgs, models_events, models_confounds = \
first_level_from_bids(data_dir, task_label, space_label, smoothing_fwhm=6,
                      img_filters=[('desc','preproc'),('dir','AP'),('dir','PA')],
                      derivatives_folder=derivatives_folder)

The data I am trying to analyze consists of two runs of task data, one run in AP and one run in PA. The full paths to my fmriprep preprocessed data files are:

'/Volumes/Pegasus/nilearn/derivatives/fmriprep/sub-XXXX/ses-01/func/sub-XXXX_ses-01_task-card_dir-AP_space-MNI152NLin2009cAsym_desc-preproc_bold.nii'

'/Volumes/Pegasus/nilearn/derivatives/fmriprep/sub-XXXX/ses-01/func/sub-XXXX_ses-01_task-card_dir-PA_space-MNI152NLin2009cAsym_desc-preproc_bold.nii'

If anybody has any insight into what might be causing this error, I’d greatly appreciate it.

Thanks!
Hannah

2

Hi, sorry for that.
What if you remove the (‘dir’, ‘AP’), (‘dir’, ‘PA’) from img_filters ?
Best,
Bertrand

3

Removing (‘dir’,‘AP’),(‘dir’,‘PA’) from img_filters results in the following error:

ValueError: More than one nifti image found for the same ses 01, while no additional run specification present. Please verify that the desc_label and space_label labels corresponding to the BIDS spec were correctly specified.

The entire traceback:

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
/var/folders/5s/c4kkvs2j0glc78dbm7n6d75h0000gp/T/ipykernel_77929/2981758697.py in <module>
      5 derivatives_folder = '/Volumes/Pegasus/nilearn/derivatives/fmriprep'
      6 models, models_run_imgs, models_events, models_confounds = \
----> 7 first_level_from_bids(data_dir, task_label, space_label, smoothing_fwhm=6,
      8                       img_filters=[('desc','preproc')],
      9                       derivatives_folder=derivatives_folder)

~/opt/anaconda3/lib/python3.9/site-packages/nilearn/glm/first_level/first_level.py in first_level_from_bids(dataset_path, task_label, space_label, img_filters, t_r, slice_time_ref, hrf_model, drift_model, high_pass, drift_order, fir_delays, min_onset, mask_img, target_affine, target_shape, smoothing_fwhm, memory, memory_level, standardize, signal_scaling, noise_model, verbose, n_jobs, minimize_memory, derivatives_folder)
    998                 elif '_ses-' in img_dict['file_basename']:
    999                     if img_dict['ses'] in run_check_list:
-> 1000                         raise ValueError(
   1001                             'More than one nifti image '
   1002                             'found for the same ses %s, while '

ValueError: More than one nifti image found for the same ses 01, while no additional run specification present. Please verify that the desc_label and space_label labels corresponding to the BIDS spec were correctly specified.
4

Hm. Then, with only(‘dir’, ‘AP’), does it work ?

5

It’s very strange. If I set img_filters=[('dir','AP')], the error I receive is:

ValueError: 2 events.tsv files found for 1 bold files. Same number of event files as the number of runs is expected

But if I set img_filters=[('dir','AP'), ('dir','PA')], the error is:

ValueError: 2 events.tsv files found for 0 bold files. Same number of event files as the number of runs is expected

Not setting any image filters results in:

ValueError: More than one nifti image found for the same ses 01, while no additional run specification present. Please verify that the desc_label and space_label labels corresponding to the BIDS spec were correctly specified.

6

I see in the doc “Only one filter per field allowed.”, which may explain the odd behavior.
I’m afraid that you hit a deep bug. I’ll try to look more deeply…
Best,
Bertrand

7

Interesting. Thanks for looking into this.

We have other task data in folder (_task-rest & _task-ssrt) both in AP and PA, so perhaps the task_label parameter isn’t being detected properly?

8

I suspect that this kind of bug should be fixed with latest version of Nilearn but if not feel free to open an issue on the repository