├── .circleci └── config.yml ├── .hadolint.yaml ├── .idea └── vcs.xml ├── .pre-commit-config.yaml ├── Dockerfile ├── LICENSE ├── README.md ├── run.py └── version /.circleci/config.yml: -------------------------------------------------------------------------------- 1 | --- 2 | version: 2.1 3 | jobs: 4 | build: 5 | machine: 6 | image: ubuntu-2204:2022.10.2 7 | steps: 8 | - checkout 9 | - run: 10 | name: Get test data 11 | command: | 12 | wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/utils/get_data_from_osf.sh 13 | bash get_data_from_osf.sh ds005-deriv-light 14 | - run: 15 | name: Build Docker image 16 | command: | 17 | wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/circleci/build_docker.sh 18 | bash build_docker.sh 19 | - persist_to_workspace: 20 | root: /home/circleci 21 | paths: 22 | - data/ds005-deriv-light 23 | - docker/image.tar 24 | 25 | test: 26 | machine: 27 | image: ubuntu-2204:2022.10.2 28 | steps: 29 | - attach_workspace: 30 | at: /tmp/workspace 31 | - run: docker load -i /tmp/workspace/docker/image.tar 32 | - run: mkdir -p ${HOME}/outputs 33 | - run: 34 | name: run participant 01 35 | command: | 36 | docker run -ti --rm --read-only \ 37 | -v /tmp:/tmp -v /var/tmp:/var/tmp \ 38 | -v /tmp/workspace/data/ds005-deriv-light/derivatives:/bids_dataset \ 39 | -v ${HOME}/outputs:/outputs \ 40 | bids/"${CIRCLE_PROJECT_REPONAME,,}" \ 41 | /bids_dataset \ 42 | /outputs \ 43 | participant \ 44 | --participant_label 01 \ 45 | --task mixedgamblestask \ 46 | --run 01 47 | no_output_timeout: 6h 48 | - run: 49 | name: run participant 02 50 | command: | 51 | docker run -ti --rm --read-only \ 52 | -v /tmp:/tmp -v /var/tmp:/var/tmp \ 53 | -v /tmp/workspace/data/ds005-deriv-light/derivatives:/bids_dataset \ 54 | -v ${HOME}/outputs:/outputs \ 55 | bids/"${CIRCLE_PROJECT_REPONAME,,}" \ 56 | /bids_dataset \ 57 | /outputs \ 58 | participant \ 59 | --participant_label 02 \ 60 | --task mixedgamblestask \ 61 | --run 01 62 | no_output_timeout: 6h 63 | - run: 64 | name: run participant 03 65 | command: | 66 | docker run -ti --rm --read-only \ 67 | -v /tmp:/tmp -v /var/tmp:/var/tmp \ 68 | -v /tmp/workspace/data/ds005-deriv-light/derivatives:/bids_dataset \ 69 | -v ${HOME}/outputs:/outputs \ 70 | bids/"${CIRCLE_PROJECT_REPONAME,,}" \ 71 | /bids_dataset \ 72 | /outputs \ 73 | participant \ 74 | --participant_label 03 \ 75 | --task mixedgamblestask \ 76 | --run 01 77 | no_output_timeout: 6h 78 | - run: 79 | name: run group 80 | command: | 81 | docker run -ti --rm --read-only \ 82 | -v /tmp:/tmp -v /var/tmp:/var/tmp \ 83 | -v /tmp/workspace/data/ds005-deriv-light/derivatives:/bids_dataset \ 84 | -v ${HOME}/outputs:/outputs \ 85 | bids/"${CIRCLE_PROJECT_REPONAME,,}" \ 86 | /bids_dataset \ 87 | /outputs \ 88 | group 89 | no_output_timeout: 6h 90 | 91 | deploy: 92 | machine: 93 | image: ubuntu-2204:2022.10.2 94 | steps: 95 | - attach_workspace: 96 | at: /tmp/workspace 97 | - run: docker load -i /tmp/workspace/docker/image.tar 98 | - run: 99 | name: push to dockerhub 100 | command: | 101 | wget https://raw.githubusercontent.com/bids-apps/maintenance-tools/main/circleci/push_docker.sh 102 | bash push_docker.sh 103 | 104 | workflows: 105 | build-test-deploy: 106 | jobs: 107 | - build 108 | - test: 109 | requires: 110 | - build 111 | - deploy: 112 | context: 113 | - dockerhub 114 | requires: 115 | - test 116 | filters: 117 | tags: 118 | only: /.*/ 119 | 120 | # VS Code Extension Version: 1.5.1 121 | -------------------------------------------------------------------------------- /.hadolint.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | ignored: 3 | - DL3003 4 | - DL3008 5 | -------------------------------------------------------------------------------- /.idea/vcs.xml: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- 1 | --- 2 | # See https://pre-commit.com for more information 3 | # See https://pre-commit.com/hooks.html for more hooks 4 | 5 | repos: 6 | - repo: https://github.com/pre-commit/pre-commit-hooks 7 | rev: v5.0.0 8 | hooks: 9 | - id: trailing-whitespace 10 | - id: end-of-file-fixer 11 | - id: check-yaml 12 | - id: check-json 13 | - id: check-added-large-files 14 | - id: check-case-conflict 15 | - id: check-merge-conflict 16 | 17 | 18 | - repo: https://github.com/jumanjihouse/pre-commit-hook-yamlfmt 19 | rev: 0.2.3 20 | hooks: 21 | - id: yamlfmt 22 | args: [--mapping, '2', --sequence, '2', --offset, '0'] 23 | 24 | 25 | - repo: https://github.com/hadolint/hadolint 26 | rev: v2.13.1-beta 27 | hooks: 28 | - id: hadolint-docker 29 | name: Lint Dockerfiles 30 | description: Runs hadolint Docker image to lint Dockerfiles 31 | language: docker_image 32 | types: [dockerfile] 33 | entry: ghcr.io/hadolint/hadolint hadolint 34 | 35 | ci: 36 | skip: [hadolint-docker] 37 | -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- 1 | FROM ubuntu:18.04 2 | 3 | # Prepare environment 4 | RUN apt-get update -qq && \ 5 | apt-get install -qq -y --no-install-recommends \ 6 | apt-utils \ 7 | autoconf \ 8 | build-essential \ 9 | bzip2 \ 10 | ca-certificates \ 11 | curl \ 12 | git \ 13 | libtool \ 14 | lsb-release \ 15 | netbase \ 16 | pkg-config \ 17 | unzip \ 18 | xvfb && \ 19 | apt-get clean && \ 20 | rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* 21 | 22 | ENV DEBIAN_FRONTEND="noninteractive" \ 23 | LANG="en_US.UTF-8" \ 24 | LC_ALL="en_US.UTF-8" 25 | 26 | # PyMVPA 27 | RUN apt-get update -qq && \ 28 | apt-get install -qq -y --no-install-recommends python2.7 && \ 29 | apt-get clean && \ 30 | rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* 31 | 32 | RUN apt-get update -qq && \ 33 | mkdir /dev/fuse && \ 34 | chmod 777 /dev/fuse && \ 35 | apt-get install -qq -y --no-install-recommends \ 36 | python-mvpa2 && \ 37 | apt-get clean && \ 38 | rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* 39 | 40 | RUN mkdir -p /code 41 | COPY run.py /code/run.py 42 | 43 | COPY version /version 44 | 45 | ENTRYPOINT ["/code/run.py"] 46 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | Apache License 2 | Version 2.0, January 2004 3 | http://www.apache.org/licenses/ 4 | 5 | TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION 6 | 7 | 1. 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The text should be enclosed in the appropriate 184 | comment syntax for the file format. We also recommend that a 185 | file or class name and description of purpose be included on the 186 | same "printed page" as the copyright notice for easier 187 | identification within third-party archives. 188 | 189 | Copyright {yyyy} {name of copyright owner} 190 | 191 | Licensed under the Apache License, Version 2.0 (the "License"); 192 | you may not use this file except in compliance with the License. 193 | You may obtain a copy of the License at 194 | 195 | http://www.apache.org/licenses/LICENSE-2.0 196 | 197 | Unless required by applicable law or agreed to in writing, software 198 | distributed under the License is distributed on an "AS IS" BASIS, 199 | WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 200 | See the License for the specific language governing permissions and 201 | limitations under the License. 202 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | ## Hyperalignment BIDS App (WiP) 2 | 3 | ### Description 4 | 5 | Hyperalignment is a functional alignment method that aligns subjects' brain data in a 6 | high-dimensional space of voxels/features. We showed that this alignment aligns subjects 7 | at a fine-scale affording between-subject decoding and encoding 8 | [Guntupalli et al. 2016](http://cercor.oxfordjournals.org/content/26/6/2919). This app runs searchlight 9 | hyperalignment, which runs hyperalignment in multiple searchlights across the whole brain and 10 | aggregates them into a single transformation per subject. 11 | For now, many parameters such as searchlight size, sparsity of centers, etc., are fixed. 12 | Please use PyMVPA to modify these and other parameters for your use case. 13 | 14 | ### Documentation 15 | 16 | For a detailed documentation and examples, please see: 17 | Hyperalignment in a ROI: 18 | http://www.pymvpa.org/generated/mvpa2.algorithms.hyperalignment.Hyperalignment.html 19 | Searchlight Hyperalignment: 20 | https://github.com/PyMVPA/PyMVPA/blob/master/mvpa2/algorithms/searchlight_hyperalignment.py 21 | Example in PyMVPA: 22 | http://www.pymvpa.org/examples/hyperalignment.html 23 | 24 | ### Acknowledgements 25 | 26 | If you use this in your project, please cite [Guntupalli et al. 2016](http://cercor.oxfordjournals.org/content/26/6/2919). 27 | 28 | ### Report Bugs/Issues 29 | 30 | Please use PyMVPA on github to report any bugs/issues or to contribute: 31 | https://github.com/PyMVPA/PyMVPA 32 | 33 | ### Usage 34 | 35 | usage: run.py [-h] 36 | [--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...] 37 | --task TASK_LABEL --run RUN_LABEL] 38 | bids_dir output_dir {participant,group} 39 | 40 | Example BIDS App entrypoint script. 41 | 42 | positional arguments: 43 | bids_dir The directory with the input dataset formatted 44 | according to the BIDS standard. 45 | output_dir The directory where the output files should be stored. 46 | If you are running group level analysis this folder 47 | should be prepopulated with the results of 48 | theparticipant level analysis. 49 | {participant,group} Level of the analysis that will be performed. Multiple 50 | participant level analyses can be run independently 51 | (in parallel). 52 | 53 | optional arguments: 54 | -h, --help show this help message and exit 55 | --participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...] 56 | The label(s) of the participant(s) that should be 57 | analyzed. The label corresponds to 58 | sub- from the BIDS spec (so it does 59 | not include "sub-"). If this parameter is not provided 60 | all subjects should be analyzed. Multiple participants 61 | can be specified with a space separated list. 62 | --task TASK_LABEL Name of the task that should be used for hyperalignment. 63 | This correspnds to task- from the BIDS spec 64 | (so it does not include "task-"). 65 | --run RUN_LABEL Name of the run that should be used for hyperalignment. 66 | This correspnds to run- from the BIDS spec 67 | (so it does not include "run-"). 68 | 69 | 70 | Participant level mode prepares the data for hyperalignment. 71 | For now, it loads the data from nifti image into PyMVPA readable datasets after applying 72 | brain mask. In future, this will be modified to compute individual subject connectomes. 73 | 74 | docker run -i --rm \ 75 | -v /Users/swaroop/ds005-deriv/derivatives:/bids_dataset \ 76 | -v /Users/swaroop/outputs:/outputs \ 77 | bids/hyperalignment \ 78 | /bids_dataset /outputs participant \ 79 | --task mixedgamblestask --run 01 --participant_label 01 80 | 81 | After running participant level (potentially in parallel), group level analysis 82 | runs hyperalignment and saves transformation parameters. 83 | 84 | docker run -i --rm -v \ 85 | /Users/swaroop/ds005-deriv/derivatives:/bids_dataset \ 86 | -v /Users/swaroop/outputs:/outputs \ 87 | bids/hyperalignment \ 88 | /bids_dataset /outputs group 89 | 90 | ### Special requirements 91 | 92 | Hyperalignment works on preprocessed data with all the subjects' data aligned to the same template. 93 | 94 | ### Relevant references 95 | 96 | 1. Guntupalli, J. S., Hanke, M., Halchenko, Y. O., Connolly, A. C., Ramadge, P. J. & Haxby, J. V. (2016). A Model of Representational Spaces in Human Cortex. Cerebral Cortex. 97 | DOI: http://dx.doi.org/10.1093/cercor/bhw068 98 | 2. Haxby, J. V., Guntupalli, J. S., Connolly, A. C., Halchenko, Y. O., Conroy, B. R., Gobbini, M. I., Hanke, M. & Ramadge, P. J. (2011). A Common, High-Dimensional Model of the Representational Space in Human Ventral Temporal Cortex. Neuron, 72, 404–416. 99 | DOI: http://dx.doi.org/10.1016/j.neuron.2011.08.026 100 | -------------------------------------------------------------------------------- /run.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | import argparse 3 | import os 4 | from glob import glob 5 | from mvpa2.suite import * 6 | from mvpa2.base.hdf5 import h5save, h5load 7 | from mvpa2.algorithms.searchlight_hyperalignment import SearchlightHyperalignment 8 | from mvpa2.datasets.mri import fmri_dataset 9 | from mvpa2.mappers.zscore import zscore 10 | 11 | 12 | parser = argparse.ArgumentParser(description='Example BIDS App entrypoint script.') 13 | parser.add_argument('bids_dir', help='The directory with the input dataset ' 14 | 'formatted according to the BIDS standard.') 15 | parser.add_argument('output_dir', help='The directory where the output files ' 16 | 'should be stored. If you are running group level analysis ' 17 | 'this folder should be prepopulated with the results of the' 18 | 'participant level analysis.') 19 | parser.add_argument('analysis_level', 20 | help='Level of the analysis that will be performed. ' 21 | 'Multiple participant level analyses can be run independently ' 22 | '(in parallel) using the same output_dir.', 23 | choices=['participant', 'group']) 24 | parser.add_argument('--participant_label', 25 | help='The label(s) of the participant(s) that should be analyzed. The label ' 26 | 'corresponds to sub- from the BIDS spec ' 27 | '(so it does not include "sub-"). If this parameter is not ' 28 | 'provided all subjects should be analyzed. Multiple ' 29 | 'participants can be specified with a space separated list.', 30 | nargs="+") 31 | parser.add_argument('--task', 32 | help='Task from which the data is used for deriving hyperalignment ' 33 | 'parameters') 34 | parser.add_argument('--run', 35 | help='Run or runs to be used for deriving hyperalignment parameters') 36 | 37 | args = parser.parse_args() 38 | 39 | subjects_to_analyze = [] 40 | # only for a subset of subjects 41 | if args.participant_label: 42 | subjects_to_analyze = args.participant_label 43 | # for all subjects 44 | else: 45 | subject_dirs = glob(os.path.join(args.bids_dir, "sub-*")) 46 | subjects_to_analyze = [subject_dir.split("-")[-1] for subject_dir in subject_dirs] 47 | 48 | """ 49 | At the participant level, load nifti data using mask and store it as hdf5 file. 50 | This can be adapted to compute connectomes later. 51 | """ 52 | 53 | 54 | def prepare_subject_for_hyperalignment(subject_label, bold_fname, mask_fname, out_dir): 55 | print('Loading data %s with mask %s' % (bold_fname, mask_fname)) 56 | ds = fmri_dataset(samples=bold_fname, mask=mask_fname) 57 | zscore(ds, chunks_attr=None) 58 | out_fname = os.path.join(out_dir, 'sub-%s_data.hdf5' % subject_label) 59 | print('Saving to %s' % out_fname) 60 | h5save(out_fname, ds) 61 | 62 | 63 | def run_hyperalignment(subjects_to_analyze, out_dir): 64 | # Load subject data 65 | ds_all = [] 66 | for subject_label in subjects_to_analyze: 67 | ds_all.append(h5load('%s/sub-%s_data.hdf5' % (out_dir, subject_label))) 68 | # Initialize searchlight hyperalignment 69 | slhyper = SearchlightHyperalignment(radius=2, nblocks=10, sparse_radius=5, 70 | dtype='float16') 71 | hmappers = slhyper(ds_all) 72 | return hmappers 73 | 74 | 75 | # This can be subject-level and be applied in parallel 76 | def apply_hyperalignment(): 77 | raise NotImplementedError 78 | 79 | 80 | """ 81 | Helper functions to save and load mappers 82 | """ 83 | 84 | 85 | def save_mappers(hmappers, fname): 86 | h5save(fname, hmappers) 87 | 88 | 89 | def load_mappers(fname): 90 | return h5load(fname) 91 | 92 | # running participant level 93 | 94 | if args.analysis_level == "participant": 95 | # sub-01_task-mixedgamblestask_run-02_bold_hmc_mni.nii.gz 96 | prefixes = [] 97 | task_prefix = 'task-%s' % args.task 98 | prefixes.append(task_prefix) 99 | run_prefix = 'run-%s' % args.run 100 | prefixes.append(run_prefix) 101 | # XXX TODO Expose this option outside? 102 | preproc_prefix = 'bold_hmc_mni' 103 | prefixes.append(preproc_prefix) 104 | # find all T1s and skullstrip them 105 | prefix = '_'.join(prefixes) 106 | for subject_label in subjects_to_analyze: 107 | bold_fname = 'sub-%s_%s'%(subject_label, prefix) 108 | bold_fname = os.path.join(args.bids_dir, "sub-%s" % subject_label, 109 | "func", bold_fname) 110 | mask_fname = '%s_bmask.nii.gz' % bold_fname 111 | bold_fname = '%s.nii.gz' % bold_fname 112 | prepare_subject_for_hyperalignment(subject_label, bold_fname, mask_fname, 113 | args.output_dir) 114 | 115 | # running group level 116 | elif args.analysis_level == "group": 117 | """ 118 | Load data (timeseries or connectomes) stored in first-level 119 | and run hyperalignment. Spit out mappers. 120 | """ 121 | hmappers = run_hyperalignment(subjects_to_analyze, out_dir=args.output_dir) 122 | hmappers_fname = os.path.join(args.output_dir, 'hmappers.hdf5') 123 | save_mappers(hmappers=hmappers, fname=hmappers_fname) 124 | with open(os.path.join(args.output_dir, "Transformation_matrix_shapes.txt"), 'w') as fp: 125 | for hm in hmappers: 126 | fp.write("Transformation shape" 127 | " and non-zero elements : %s %d" % ( (hm.proj.shape,), hm.proj.data.size)) 128 | -------------------------------------------------------------------------------- /version: -------------------------------------------------------------------------------- 1 | dev 2 | --------------------------------------------------------------------------------