Nifti not a 4D volume

[srithetree]

Input parameter is a 4D BOLD functional nifti file but it does not recognize it as 4 dimensional.

Expected Behavior

One would expect it to recognize it as 4D and continue to regression.

Actual Behavior

It stops and provides the error: "ValueError: Provided functional file /home/sri/CVR/derivatives/fmriprep/sub-scd026/ses-02/func/sub-scd026_ses-02_task-cvr_desc-preproc_bold.nii.gz is not a 4D file!"

Full error output:
phys2cvr -i /home/sri/CVR/derivatives/fmriprep/sub-scd026/ses-02/func/sub-scd026_ses-02_task-cvr_desc-preproc_bold.nii.gz -o /home/sri/CVR/sri/test -m /home/sri/CVR/derivatives/fmriprep/sub-scd026/ses-02/func/sub-scd026_ses-02_task-cvr_desc-brain_mask.nii.gz -co2 /home/sri/CVR/sri/scd026_co2.csv -pk /home/sri/CVR/sri/scd026_co2_pidx.csv -fr 95.051 -tlen 19.78 -ntrial 5
INFO Currently running phys2cvr version 0.15.0
INFO Input file is /home/sri/CVR/derivatives/fmriprep/sub-scd026/ses-02/func/sub-scd026_ses-02_task-cvr_desc-preproc_bold.nii.gz
WARNING Changing type of variable trial_len from <class 'float'> to int
INFO Loading /home/sri/CVR/derivatives/fmriprep/sub-scd026/ses-02/func/sub-scd026_ses-02_task-cvr_desc-preproc_bold.nii.gz
WARNING /home/sri/CVR/derivatives/fmriprep/sub-scd026/ses-02/func/sub-scd026_ses-02_task-cvr_desc-preproc_bold.nii.gz has more than 3 dimensions. Removing D > 3.
Traceback (most recent call last):
File "/net/rc-fs-nfs.tch.harvard.edu/ifs/RC-FS-PROD/Data/Shares/FNNDSC-e2/neuro/labs/grantlab/research/CVR/venv/bin/phys2cvr", line 8, in
sys.exit(_main())
File "/net/rc-fs-nfs.tch.harvard.edu/ifs/RC-FS-PROD/Data/Shares/FNNDSC-e2/neuro/labs/grantlab/research/CVR/venv/lib/python3.8/site-packages/phys2cvr/phys2cvr.py", line 606, in _main
phys2cvr(**vars(options))
File "/net/rc-fs-nfs.tch.harvard.edu/ifs/RC-FS-PROD/Data/Shares/FNNDSC-e2/neuro/labs/grantlab/research/CVR/venv/lib/python3.8/site-packages/phys2cvr/phys2cvr.py", line 278, in phys2cvr
raise ValueError(f'Provided functional file {fname_func} is not a 4D file!')
ValueError: Provided functional file /home/sri/CVR/derivatives/fmriprep/sub-scd026/ses-02/func/sub-scd026_ses-02_task-cvr_desc-preproc_bold.nii.gz is not a 4D file!

Steps to Reproduce the Problem

1. Give it this path and run the command
2.
3.

Specifications

- Python version: 
- phys2bids version:
- Platform:

Possible solution

[dittothat]

Hi Stefano,
Sri is a medical student intern working with me this summer. I looked at this with him a bit, and on first glance at the underlying code don't know why this line

phys2cvr/phys2cvr/phys2cvr.py

Line 276 in 6713a5d

func, dmask, img = io.load_nifti_get_mask(fname_func)

is left to the default of dim=3. I am probably reading the code incorrectly.
Thanks, Jeff

[smoia]

Hey there @srithetree @dittothat this should be fixed now - thank you for the hint on where to check.
If it still doesn't work, would you be able to send me the file to make some trials?