AFNI 3D Whole-Brain Correlation Map (3dTcorrMap)¶
Library: AFNI | Docker Image: brainlife/afni
Function¶
Computes various whole-brain voxelwise correlation metrics including average correlation and global connectivity.
Modality: 4D fMRI NIfTI/AFNI time series plus brain mask.
Typical Use: Global connectivity metrics, whole-brain correlation exploration.
Key Parameters¶
-input (4D data), -mask (brain mask), -Mean (mean correlation map), -Hist (histogram outputs)
Key Points¶
Computes every-voxel-to-every-voxel correlations. Memory intensive.
Inputs¶
| Name | Type | Required | Label | Flag |
|---|---|---|---|---|
input |
File |
Yes | Input 3D+time dataset | -input |
seed |
File |
No | Seed 3D+time dataset for cross-correlation | -seed |
mask |
File |
No | Voxel mask for processing | -mask |
automask |
boolean |
No | Create mask from input dataset | -automask |
polort |
int |
No | Remove polynomial trends (-1 to 19, default 1) | -polort |
bpass |
string |
No | Bandpass frequencies L H in Hz | -bpass |
ort |
File |
No | Remove reference time series via regression | -ort |
Gblur |
double |
No | Gaussian blur kernel width in mm | -Gblur |
Mseed |
double |
No | Average seed over radius in mm | -Mseed |
Mean |
string |
No | Save average correlations prefix | -Mean |
Zmean |
string |
No | Save Fisher-transformed mean prefix | -Zmean |
Qmean |
string |
No | Save RMS correlation prefix | -Qmean |
Thresh |
string |
No | Count voxels exceeding threshold (tt pp) | -Thresh |
CorrMap |
string |
No | Output complete correlation map prefix | -CorrMap |
Aexpr |
string |
No | Average custom correlation expression (expr ppp) | -Aexpr |
Hist |
string |
No | Generate correlation histogram (N ppp) | -Hist |
Accepted Input Extensions¶
- input:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - seed:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - mask:
.nii,.nii.gz,+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - ort:
.1D,.txt
Outputs¶
| Name | Type | Glob Pattern |
|---|---|---|
mean_corr |
File |
$(inputs.Mean)+orig.HEAD, $(inputs.Mean)+tlrc.HEAD |
zmean_corr |
File |
$(inputs.Zmean)+orig.HEAD, $(inputs.Zmean)+tlrc.HEAD |
corrmap |
File |
$(inputs.CorrMap)+orig.HEAD, $(inputs.CorrMap)+tlrc.HEAD |
log |
File |
3dTcorrMap.log |
Output Extensions¶
- mean_corr:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - zmean_corr:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK - corrmap:
+orig.HEAD,+orig.BRIK,+tlrc.HEAD,+tlrc.BRIK
Docker Tags¶
Available versions: latest, 16.3.0
Categories¶
- Functional MRI > AFNI > Connectivity