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.