charestlab / pyslicetime Goto Github PK

kendrick's slicetime ported to python

Python 83.13% MATLAB 6.22% Shell 10.65%

pyslicetime's Introduction

pyslicetime

Slice-time interpolation for fMRI data.

cubic interpolation used to resample each voxel’s time-series data to a new rate such that the same time points are obtained for all voxels. This can be useful if the trial duration is not evenly divisible by the TR, which then handles any jitter between trial onsets and slice acquisition times.

The motivation for upsampling is to exploit the intrinsic jitter between the data acquisition and the experimental paradigm.

matlab version:

An equivalent functionality exists in matlab, see: https://github.com/kendrickkay/knkutils/blob/master/timeseries/tseriesinterp.m

reference:

The logic of this procedure was introduced in the following pre-print: https://www.biorxiv.org/content/10.1101/868455v1.full.pdf

pyslicetime's People

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jk619 bh-lyu c14h19no2 marek1n

pyslicetime's Issues

store stc file in correct folder.. can fmriprep tell us where?

Missing files in sdist

It appears that the manifest is missing at least one file necessary to build
from the sdist for version 0.2. You're in good company, about 5% of other
projects updated in the last year are also missing files.

+ /tmp/venv/bin/pip3 wheel --no-binary pyslicetime -w /tmp/ext pyslicetime==0.2
Looking in indexes: http://10.10.0.139:9191/root/pypi/+simple/
Collecting pyslicetime==0.2
  Downloading http://10.10.0.139:9191/root/pypi/%2Bf/a60/ebea2a7f1052b/pyslicetime-0.2.tar.gz (6.2 kB)
    ERROR: Command errored out with exit status 1:
     command: /tmp/venv/bin/python3 -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-wheel-jtca8_3x/pyslicetime/setup.py'"'"'; __file__='"'"'/tmp/pip-wheel-jtca8_3x/pyslicetime/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-wheel-jtca8_3x/pyslicetime/pip-egg-info
         cwd: /tmp/pip-wheel-jtca8_3x/pyslicetime/
    Complete output (5 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-wheel-jtca8_3x/pyslicetime/setup.py", line 4, in <module>
        with open('requirements.txt') as reqfile:
    FileNotFoundError: [Errno 2] No such file or directory: 'requirements.txt'
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

missing file

         [Node] Finished "fmriprep_wf.single_subject_1_wf.func_preproc_ses_2_task_fmriwmrsa_run_02_wf.bold_stc_wf.slice_timing_correction".
190719-16:53:54,529 nipype.workflow INFO:
         [Node] Finished "fmriprep_wf.single_subject_1_wf.func_preproc_ses_2_task_fmriwmrsa_run_04_wf.bold_stc_wf.slice_timing_correction".
190719-16:53:55,382 nipype.workflow WARNING:
         Error while checking node hash, forcing re-run. Although this error may not prevent the workflow from running, it could indicate a major problem. Please report a new issue at https://github.com/nipy/nipype/issues adding the following information:

        Node: fmriprep_wf.single_subject_1_wf.func_preproc_ses_2_task_fmriwmrsa_run_02_wf.bold_split
        Interface: nipype.interfaces.fsl.utils.Split
        Traceback:
Traceback (most recent call last):

  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/base.py", line 338, in _local_hash_check
    cached, updated = self.procs[jobid].is_cached()

  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 296, in is_cached
    hashed_inputs, hashvalue = self._get_hashval()

  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 493, in _get_hashval
    self._get_inputs()

  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 540, in _get_inputs
    self.set_input(key, deepcopy(output_value))

  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 278, in set_input
    setattr(self.inputs, parameter, deepcopy(val))

  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/traits_extension.py", line 112, in validate
    self.info_text, value))

traits.trait_errors.TraitError: The trait 'in_file' of a SplitInputSpec instance is an existing file name, but the path  'slicetime.nii.gz' does not exist.

Error setting node input:
Node: bold_split
input: in_file
results_file: /work/fmriprep_wf/single_subject_1_wf/func_preproc_ses_2_task_fmriwmrsa_run_02_wf/bold_stc_wf/slice_timing_correction/result_slice_timing_correction.pklz
value: slicetime.nii.gz

nibabel saving problem

Node: fmriprep_wf.single_subject_1_wf.func_preproc_ses_1_task_fmriwmrsa_run_02_wf.bold_stc_wf.slice_timing_correction
Working directory: /work/fmriprep_wf/single_subject_1_wf/func_preproc_ses_1_task_fmriwmrsa_run_02_wf/bold_stc_wf/slice_timing_correction

Node inputs:

in_file = /work/fmriprep_wf/single_subject_1_wf/func_preproc_ses_1_task_fmriwmrsa_run_02_wf/bold_reference_wf/validate/sub-1_ses-1_task-fmriwmrsa_run-02_bold_valid.nii.gz
out_file =
slicetimes = [0.66, 0.0, 0.44, 0.075, 0.515, 0.1475, 0.5875, 0.295, 0.735, 0.3675, 0.8075, 0.22, 0.66, 0.0, 0.44, 0.075, 0.515, 0.1475, 0.5875, 0.295, 0.735, 0.3675, 0.8075, 0.22, 0.66, 0.0, 0.44, 0.075, 0.515, 0.1475, 0.5875, 0.295, 0.735, 0.3675, 0.8075, 0.22, 0.66, 0.0, 0.44, 0.075, 0.515, 0.1475, 0.5875, 0.295, 0.735, 0.3675, 0.8075, 0.22]
tr_new = 0.5
tr_old = 0.9

Traceback (most recent call last):
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node
result['result'] = node.run(updatehash=updatehash)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 472, in run
result = self._run_interface(execute=True)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 563, in _run_interface
return self._run_command(execute)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_command
result = self._interface.run(cwd=outdir)
File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 375, in run
runtime = self._run_interface(runtime)
File "/usr/local/miniconda/lib/python3.7/site-packages/slicetime/nipype_interface.py", line 44, in _run_interface
tr_new=self.inputs.tr_new,
File "/usr/local/miniconda/lib/python3.7/site-packages/slicetime/main.py", line 71, in run_slicetime
nib.save(corr_img, outpath)
File "/usr/local/miniconda/lib/python3.7/site-packages/nibabel/loadsave.py", line 106, in save
froot, ext, trailing = splitext_addext(filename, ('.gz', '.bz2'))
File "/usr/local/miniconda/lib/python3.7/site-packages/nibabel/filename_parser.py", line 265, in splitext_addext
if endswith(filename, ext):
File "/usr/local/miniconda/lib/python3.7/site-packages/nibabel/filename_parser.py", line 223, in _iendswith
return whole.lower().endswith(end.lower())
AttributeError: '_Undefined' object has no attribute 'lower'

    upsample_tr=upsample_tr
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/bold/stc.py", line 65, in init_bold_stc_wf
    return init_bold_stc_pyslt_wf(metadata, name, upsample_tr)
  File "/usr/local/miniconda/lib/python3.7/site-packages/fmriprep/workflows/bold/stc.py", line 156, in init_bold_stc_pyslt_wf
    (slice_timing_correction, outputnode, [('out_file', 'stc_file')]),
  File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/workflows.py", line 214, in connect
    '\n'.join(['Some connections were not found'] + infostr))
Exception: Some connections were not found
Module slice_timing_correction has no output called out_file