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cvnlab / GLMsingle

A toolbox for accurate single-trial estimates in fMRI time-series data
BSD 3-Clause "New" or "Revised" License
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Issues upsampling #119

Open andreifoldes opened 11 months ago

andreifoldes commented 11 months ago

Greetings, Trying to upsample an fmriprep'ed preproc_bold file before using glmsingle, but I get the following " requested array has an inhomogeneous shape after 1 dimensions". These have have already been slice time corrected, so I guess slicetimes should be shifted by half a TR (given fmriprep STC)?

Nonetheless, the error persists.

import os
import numpy as np
from slicetime.nipype_interface import SliceTime

# get some test data
in_file = '/test/test/bids/derivatives/fmriprep-20.2.7/fmriprep/sub-test/func/sub-test-task_run-5_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz'

# define some parameters
tr_old = 2
tr_new = 1
st = SliceTime()
st.inputs.in_file = in_file
st.inputs.tr_old = tr_old
st.inputs.tr_new = tr_new
st.inputs.out_file = os.path.join('.../tmp', 'test_upsampled.nii.gz')
data_pointer = nib.load(in_file)    
data = data_pointer.get_fdata()
x, y, z, n_times = data.shape
slicetimes = np.flip(np.arange(0, tr_old, tr_old/z))

# turn slicetimes into a list
st.inputs.slicetimes = slicetimes.tolist()
res = st.run()

Traceback (most recent call last): File "", line 1, in File "/home/xx/anaconda3/envs/spy310/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 397, in run runtime = self._run_interface(runtime) File "/home/xx/anaconda3/envs/spy310/lib/python3.10/site-packages/slicetime/nipype_interface.py", line 47, in _run_interface run_slicetime( File "/home/xx/anaconda3/envs/spy310/lib/python3.10/site-packages/slicetime/main.py", line 50, in run_slicetime new_slice_ts = tseriesinterp(this_slice_ts, File "/home/xx/anaconda3/envs/spy310/lib/python3.10/site-packages/slicetime/tseriesinterp.py", line 104, in tseriesinterp print("numchunks",numchunks) File "/home/xx/anaconda3/envs/spy310/lib/python3.10/site-packages/slicetime/tseriesinterp.py", line 260, in chunking f = [] ValueError: setting an array element with a sequence. The requested array has an inhomogeneous shape after 1 dimensions. The detected shape was (20,) + inhomogeneous part.

iancharest commented 3 months ago

I have now made a commit to pyslicetime fixing the chunking. @andreifoldes Can you check whether this fixes your issue?