AFNI 3D Network Correlation Matrix (3dNetCorr)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Computes pairwise correlation matrices between ROI time series extracted from a parcellation atlas.
Modality: 4D fMRI NIfTI/AFNI time series plus integer-labeled parcellation volume.
Typical Use: Creating functional connectivity matrices from parcellations.
Key Parameters¶
-inset (4D time series), -in_rois (parcellation), -prefix (output), -fish_z (Fisher z-transform), -ts_out (output time series)
Key Points¶
Outputs correlation matrix as text file. Use -fish_z for Fisher z-transformed values.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
prefix |
string |
Yes | Output file name prefix | -prefix |
inset |
File |
Yes | Input 4D time series dataset | -inset |
in_rois |
File |
Yes | ROI mask with distinct integer labels | -in_rois |
mask |
File |
No | Brain mask for correlation calculation | -mask |
fish_z |
boolean |
No | Fisher Z-transform correlation coefficients | -fish_z |
part_corr |
boolean |
No | Calculate partial correlation matrices | -part_corr |
ts_out |
boolean |
No | Output mean time series per ROI | -ts_out |
ts_label |
boolean |
No | Insert ROI label at start of each time series line | -ts_label |
ts_indiv |
boolean |
No | Create directories with individual ROI time series | -ts_indiv |
ts_wb_corr |
boolean |
No | Generate whole brain correlation maps per ROI | -ts_wb_corr |
ts_wb_Z |
boolean |
No | Generate whole brain Fisher Z-score maps per ROI | -ts_wb_Z |
weight_ts |
File |
No | Apply weights to ROI time series | -weight_ts |
weight_corr |
File |
No | Apply weights for weighted Pearson correlation | -weight_corr |
nifti |
boolean |
No | Output maps as NIFTI instead of BRIK/HEAD | -nifti |
push_thru_many_zeros |
boolean |
No | Continue even with >10% null time series in ROIs | -push_thru_many_zeros |
allow_roi_zeros |
boolean |
No | Permit ROIs with all-zero time series | -allow_roi_zeros |
automask_off |
boolean |
No | Disable automatic masking | -automask_off |
Accepted Input Extensions¶
- inset:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - in_rois:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - mask:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - weight_ts:
.1D,.txt - weight_corr:
.1D,.txt
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
correlation_matrix |
File |
$(inputs.prefix)_000.netcc |
time_series |
File |
$(inputs.prefix)_000.netts |
wb_corr_maps |
File[] |
$(inputs.prefix)_*_000_WB*.nii*, $(inputs.prefix)_*_000_WB*+orig.* |
log |
File |
$(inputs.prefix).log |
Output Extensions¶
- correlation_matrix:
.netcc - time_series:
.netts - wb_corr_maps:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Functional MRI > AFNI > Connectivity