Shared Response Model (SRM) from the Brain Imaging Analysis Kit (BrainIAK).
The Shared Response Model (SRM) is a method for aligning fMRI scans from several subjects by assuming similar functional behavior in the brain. The voxels of each subject are mapped to voxels of other subjects by projecting the information from each subject into a low-dimensional space.
http://brainiak.org/docs/brainiak.funcalign.html
Open a GitHub issue in BrainIAK (if the issue is about SRM) or here (if the issue is about this wrapper app). We also welcome all kinds of contributions to BrainIAK.
Please cite the following papers based on which SRM is implemented.
"A Reduced-Dimension fMRI Shared Response Model", P.-H. Chen, J. Chen, Y. Yeshurun-Dishon, U. Hasson, J. Haxby, P. Ramadge, Advances in Neural Information Processing Systems (NIPS), 2015. http://papers.nips.cc/paper/5855-a-reduced-dimension-fmri-shared-response-model
"Enabling Factor Analysis on Thousand-Subject Neuroimaging Datasets", Michael J. Anderson, Mihai Capotă, Javier S. Turek, Xia Zhu, Theodore L. Willke, Yida Wang, Po-Hsuan Chen, Jeremy R. Manning, Peter J. Ramadge, Kenneth A. Norman, IEEE Big Data, 2016. https://doi.org/10.1109/BigData.2016.7840719
This App has the following command line arguments:
usage: run.py [-h]
[--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]]
[--run RUN] [--task TASK] [--preproc PREPROC] [--mask MASK]
[--iterations ITERATIONS] [--features FEATURES]
bids_dir output_dir {participant,group}
Shared Response Model runner
positional arguments:
bids_dir Input directory
output_dir Output directory
{group} Level of the analysis that will be performed
optional arguments:
-h, --help show this help message and exit
--participant_label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]
Labels for participants to be analyzed (default: None)
--run RUN Run to be analyzed (default: 01)
--task TASK Task to be analyzed, default is any (default: *)
--preproc PREPROC Preprocessing tag, default is any (default: *)
--mask MASK Mask tag (default: bmask)
--iterations ITERATIONS
Number of iterations, default is SRM default (default:
None)
--features FEATURES Number of features, default is SRM default (default:
None)
This app requires preprocessed data with all volumes of a subject registered. It also requires masks to be present in the input data; all to-be-analyzed volumes of a subject must use the same mask.
SRM works only on group level because it is a method for aligning fMRI scans from multiple subjects.
The data must be time-synchronized, i.e., all subjects must be presented with the same stimuli with the same duration in the same order.
Multiple runs and tasks can be given ("*") if the number of voxels is the same within subject (the number of voxels can differ across subjects).