Taylor Salo tsalo

## getCodeDir.m
codeFile = mfilename('fullpath');
[codeDir, ~] = fileparts(codeFile);
codeDir = [codeDir '/'];

## cleanPath.m
function fixedPath = cleanPath(inPath)
% FORMAT fixedPath = cleanPath(inPath)
% Removes extra slashed from inPath.

[filePath, fileName, fileSuffix] = fileparts(inPath);

if isempty(fileSuffix)
  splitFile = regexp(filePath, '/', 'split');
else
  splitFile = regexp(inPath, '/', 'split');

## get_code_dir.py
"""
Get directory of script. Also, get parent directory.
"""
import os.path

code_dir = os.path.dirname(__file__)
par_dir = os.path.abspath(os.path.join(code_dir, os.path.pardir))

## allFilesExist.m
function log = allFilesExist(cellArray)
log = all(cellfun(@(X) logical(exist(X, 'file')), cellArray));
end

## coolCellFuns.m
% Dir results to cell array of file names
AllTextFiles = dir('/home/tsalo/*.txt');
cellArray = struct2cell(AllTextFiles);
cellArray = cellArray(1, :);
[allFilepaths, allFilenames, allSuffixes] = cellfun(@(X) fileparts(X), cellArray, 'UniformOutput', false);


## assign_intendedfor.py
import json
import bisect
from glob import glob
from os.path import join, splitext
from bids.grabbids import BIDSLayout
from dateutil.parser import parse

# subj_dir *must* have trailing /
subj_dir = '/scratch/tsalo006/dset/sub-01/'
sess = '01'

## nipype_lss.py
from nipype.interfaces.base import Bunch
from nipype.algorithms import modelgen
from copy import deepcopy


def lss(bunch_list):
    """Takes input Bunch list and returns list of Bunch lists with LSS regressors.
    """
    all_infos = []
    other_items = ['durations', 'amplitudes',

## tedana_decision_tree_pseudocode.py
from textwrap import dedent
import logging

LGR = logging.getLogger(__name__)


def list_to_str(lst, joiner='and'):
    if len(lst) == 1:
        return lst[0]
    elif len(lst) == 2:

## nimare_atlas_decoding.ipynb

      
              1 file
            
          
              0 forks
            
          
              0 comments
            
          
              0 stars
            
          
                tsalo
                / nimare_atlas_decoding.ipynb
            
            
              Created
              June 17, 2020 19:44
            
              
                Decoding an atlas with NiMARE v0.0.3
              
          
      Sorry, something went wrong. Reload?
      Sorry, we cannot display this file.
      Sorry, this file is invalid so it cannot be displayed.
      
          Viewer requires iframe.
      
    
## collect_fmriprep.py
"""
Collect native-space preprocessed data from fMRIPrep working directory and
copy into fMRIPrep derivatives directory, in BIDS format.

This script has only been tested on fMRIPrep v20.2.1.
It may not work with other versions.

Written by Julio Peraza (@JulioAPeraza)
"""
import argparse
	codeFile = mfilename('fullpath');
	[codeDir, ~] = fileparts(codeFile);
	codeDir = [codeDir '/'];
	function fixedPath = cleanPath(inPath)
	% FORMAT fixedPath = cleanPath(inPath)
	% Removes extra slashed from inPath.

	[filePath, fileName, fileSuffix] = fileparts(inPath);

	if isempty(fileSuffix)
	splitFile = regexp(filePath, '/', 'split');
	else
	splitFile = regexp(inPath, '/', 'split');
	"""
	Get directory of script. Also, get parent directory.
	"""
	import os.path

	code_dir = os.path.dirname(__file__)
	par_dir = os.path.abspath(os.path.join(code_dir, os.path.pardir))
	function log = allFilesExist(cellArray)
	log = all(cellfun(@(X) logical(exist(X, 'file')), cellArray));
	end
	% Dir results to cell array of file names
	AllTextFiles = dir('/home/tsalo/*.txt');
	cellArray = struct2cell(AllTextFiles);
	cellArray = cellArray(1, :);
	[allFilepaths, allFilenames, allSuffixes] = cellfun(@(X) fileparts(X), cellArray, 'UniformOutput', false);
	import json
	import bisect
	from glob import glob
	from os.path import join, splitext
	from bids.grabbids import BIDSLayout
	from dateutil.parser import parse

	# subj_dir must have trailing /
	subj_dir = '/scratch/tsalo006/dset/sub-01/'
	sess = '01'
	from nipype.interfaces.base import Bunch
	from nipype.algorithms import modelgen
	from copy import deepcopy


	def lss(bunch_list):
	"""Takes input Bunch list and returns list of Bunch lists with LSS regressors.
	"""
	all_infos = []
	other_items = ['durations', 'amplitudes',
	from textwrap import dedent
	import logging

	LGR = logging.getLogger(__name__)


	def list_to_str(lst, joiner='and'):
	if len(lst) == 1:
	return lst[0]
	elif len(lst) == 2:
	"""
	Collect native-space preprocessed data from fMRIPrep working directory and
	copy into fMRIPrep derivatives directory, in BIDS format.

	This script has only been tested on fMRIPrep v20.2.1.
	It may not work with other versions.

	Written by Julio Peraza (@JulioAPeraza)
	"""
	import argparse