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Taylor Salo tsalo

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@tsalo
tsalo / fmriprep_warp.sh
Last active Mar 28, 2022
Warp native-space tedana derivatives to standard space with fMRIPrep transforms.
View fmriprep_warp.sh
# First, let's define some paths to the fMRIPrep and tedana outputs
fmriprep_dir="/path/to/fmriprep/derivatives/of/subject"
tedana_dir="/path/to/tedana/derivatives"
# Result of denoising the scanner-space multi-echo data with tedana
file_to_warp="${tedana_dir}/sub-01_task-rest_desc-optcomDenoised_bold.nii.gz"
# Name of the standard-space denoised data file to be written out
out_file="${tedana_dir}/sub-01_task-rest_space-MNI152NLin2009cAsym_desc-optcomDenoised_bold.nii.gz"
@tsalo
tsalo / profile_nimare.py
Last active Feb 12, 2022
An ongoing effort to profile certain steps in NiMARE, including kernel transformation and meta-analysis estimation
View profile_nimare.py
"""A small job to profile kernel transformers and meta estimators in NiMARE."""
import logging
import os.path as op
import psutil
from datetime import datetime
import numpy as np
import pandas as pd
from memory_profiler import memory_usage
@tsalo
tsalo / collect_fmriprep.py
Last active Aug 18, 2021
A short script to collect echo-wise processed files from an fMRIPrep working directory.
View 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
@tsalo
tsalo / nimare_atlas_decoding.ipynb
Created Jun 17, 2020
Decoding an atlas with NiMARE v0.0.3
View nimare_atlas_decoding.ipynb
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@tsalo
tsalo / tedana_decision_tree_pseudocode.py
Last active Nov 6, 2019
Some pseudocode implementing a tedana decision tree node according to a proposed specification.
View 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:
View 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',
@tsalo
tsalo / assign_intendedfor.py
Created Apr 18, 2017
Add "IntendedFor" field to BIDS field map jsons for the associated fMRI and DWI scans based on acquisition time.
View 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'
View 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);
@tsalo
tsalo / allFilesExist.m
Created Apr 29, 2015
Check if all files in cell array exist.
View allFilesExist.m
function log = allFilesExist(cellArray)
log = all(cellfun(@(X) logical(exist(X, 'file')), cellArray));
end
@tsalo
tsalo / get_code_dir.py
Last active Aug 29, 2015
Get directory of script. Also, get parent directory. Add to the beginning of a script to help you load files in the same directory as the script. Makes projects more portable.
View 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))