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. 2013 Nov 21;7:794. doi: 10.3389/fnhum.2013.00794

Table 1.

Files produced by BrainCAT.

Filename Contents
{SUBJID}_diff.nii.gz Original DWI in NIfTI format
{SUBJID}_diff.bval Diffusion b-values text file
{SUBJID}_diff.bvec Diffusion gradients’ directions text file
{SUBJID}_diff.nii.gz Original DWI in NIfTI format
{SUBJID}_diff_b0.nii.gz b0 image of the diffusion acquisition
{SUBJID}... _eddy.nii.gz Diffusion images after eddy current and motion correction
{SUBJID}... _eddy.ecclog eddy_correct log file with the transformations applied during eddy current correction
{SUBJID}_fnc.nii.gz Original functional images in NIfTI format
{SUBJID}_... _vol.nii.gz Functional images after removal of initial volumes
{SUBJID}_... _stime.nii.gz Functional images after slice timing
{SUBJID}_... _mean.nii.gz Mean functional image
{SUBJID}_... _mcf.nii.gz Functional images after motion correction
{SUBJID}... _mcf.par Motion correction estimated parameters for translation and rotation
{SUBJID}... _rot.png Chart image with motion parameters for rotations
{SUBJID}... _trans.png Chart image with motion parameters for translations
{SUBJID}_... _smooth.nii.gz Functional images after smoothing
{SUBJID}_... _filter.nii.gz Functional images after filtering
{SUBJID}_str.nii.gz Original structural images in NIfTI format
{SUBJID}_... _bet.nii.gz Images after skull stripping
{SUBJID}_... _bet_mask.nii.gz Skull stripping brain mask
{SUBJID}_... _mni.nii.gz Normalized images
{SUBJID}_... _2str.mat Affine transformation matrix to native structural space
{SUBJID}_... _2mni.mat Affine transformation matrix to MNI standard space
{SUBJID}_... _2nat.mat Affine transformation matrix from MNI standard space to native space
melodic_IC.nii.gz 4D Melodic output file with the ICA results
component_{compID}.nii.gz Independent component extracted to be analyzed. compID is the compIDth image from the melodic_IC.nii.gz file
component_{compID}_cls.nii.gz Image containing the clusters resulting from the thresholding of the compIDth independent component
component_{compID}_roi_{roiID}.nii.gz Mask image of the cluster with roiID intensity
component_{compID}_clusterinfo.txt Clusters data text file
component_{compID}_localmaxinfo.txt Local maxima data text file
component_{compID}_atlasregions.txt Local maxima
{SUBJID}_roi_{roi1ID}_roi_{roi2ID}.trk Local maxima corresponding atlas regions
{SUBJID}_dwi.nii.gz Diffusion images used for tensor estimation
{SUBJID}_tensor.nii.gz Estimated tensor data
{SUBJID}_adc.nii.gz MD scalar map
{SUBJID}_e1.nii.gz First eigenvalue scalar map
{SUBJID}_e2nii.gz Second eigenvalue scalar map
{SUBJID}_e3.nii.gz Third eigenvalue scalar map
{SUBJID}_v1.nii.gz First eigenvector data
{SUBJID}_v2.nii.gz Second eigenvector data
{SUBJID}_v3.nii.gz Third eigenvector data
{SUBJID}_fa.nii.gz FA scalar map
{SUBJID}_fa_color.nii.gz Colored FA scalar map
{SUBJID}.trk Whole brain tractography file
{SUBJID}_roi_{roi1ID}_roi_{roi2ID}.trk Track file containing the tracks that connect ROIs roi1ID and roi2ID
{SUBJID}_roi_{roi1ID}_roi_{roi2ID}_vol.nii NIfTI image representative of the tracks that connect ROIs roi1ID and roi2ID
{SUBJID}_roi_{roi1ID}_roi_{roi2ID}_mni.trk Track file transformed into MNI standard space
{SUBJID}_tractresults.txt Tractography results text file
grouptrack_roi_{roi1ID}_roi_{roi2ID}.trk Cross-subject combined tracts connecting ROIs roi1ID and roi2ID

Between braces words refer to the corresponding IDs (i.e., SUBJID, id of the subject being analyzed; compID, number of the independent component; roiID, roi1ID, and roi2ID: intensity value of the ROI). Ellipsis represents any combination of suffixes, depending on the workflow settings.