Key Output Files Reference
All paths below are relative to <path>/<subject_id>/analysis/anatMRI/.
T1 Native Space
| File |
Description |
T1/processed/data/T1.nii.gz |
Cropped, reoriented T1 (not bias-corrected) |
T1/processed/data/T1_brain.nii.gz |
Skull-stripped T1 |
T1/processed/data/T1_brain_mask.nii.gz |
Binary brain mask |
T1/processed/data/T1_unbiased.nii.gz |
Bias-corrected whole-head T1 |
T1/processed/data/T1_unbiased_brain.nii.gz |
Bias-corrected skull-stripped T1 |
T1 Standard Space
| File |
Description |
T1/processed/data2std/T1_2_std.nii.gz |
T1 in MNI152 1mm (linear registration) |
T1/processed/data2std/T1_2_std_brain_lin.nii.gz |
Brain-only T1 in MNI (linear) |
T1/processed/data2std/T1_2_std_warped.nii.gz |
T1 in MNI152 1mm (non-linear, RegType 2/3) |
T1/processed/data2std/T1_2_std_brain_warped.nii.gz |
Brain-only T1 in MNI (non-linear) |
| File |
Description |
T1/preproc/reg/T1_2_std.mat |
T1 → MNI linear affine |
T1/preproc/reg/std_2_T1.mat |
MNI → T1 linear affine (inverse) |
T1/preproc/reg/T1_2_std_warp_field.nii.gz |
T1 → MNI non-linear warp field |
T1/preproc/reg/T1_2_std_warp_coeff.nii.gz |
FNIRT warp coefficients (RegType 2 only) |
T1/preproc/reg/T1_2_std_warp_jac.nii.gz |
Jacobian of non-linear warp (RegType 2 only) |
T1/preproc/reg/std_2_T1_warp_field.nii.gz |
MNI → T1 inverse warp field |
Bias Field
| File |
Description |
T1/preproc/bias/T1_brain_bias.nii.gz |
FAST-estimated bias field |
Tissue Segmentation
Single-Channel (T1 only)
| File |
Description |
T1/processed/seg/tissue/sing_chan/T1_pve_CSF.nii.gz |
CSF partial volume estimate |
T1/processed/seg/tissue/sing_chan/T1_pve_GM.nii.gz |
Grey matter partial volume estimate |
T1/processed/seg/tissue/sing_chan/T1_pve_WM.nii.gz |
White matter partial volume estimate |
T1/processed/seg/tissue/sing_chan/T1_CSF_mask.nii.gz |
Binary CSF mask (PVE > 0.5) |
T1/processed/seg/tissue/sing_chan/T1_GM_mask.nii.gz |
Binary grey matter mask |
T1/processed/seg/tissue/sing_chan/T1_WM_mask.nii.gz |
Binary white matter mask |
T1/processed/seg/tissue/sing_chan/T1_pveseg.nii.gz |
FAST hard segmentation (integer labels) |
T1/processed/seg/tissue/sing_chan/T1_seg.nii.gz |
FAST segmentation map |
Multi-Channel (T1 + T2, if T2 provided)
| File |
Description |
T1/processed/seg/tissue/multi_chan/T1_pve_CSF.nii.gz |
Joint FAST CSF PVE |
T1/processed/seg/tissue/multi_chan/T1_pve_GM.nii.gz |
Joint FAST GM PVE |
T1/processed/seg/tissue/multi_chan/T1_pve_WM.nii.gz |
Joint FAST WM PVE |
Brain Volume (SIENAX)
| File |
Description |
T1/preproc/SIENAX/report.sienax |
Brain volume report with VSCALING, pgrey, vcsf, GREY, WHITE, BRAIN in mm³ |
Cortical Reconstruction
| File |
Description |
T1/processed/FreeSurfer/ |
FreeSurfer recon-all subject directory (if --freesurfer) |
T1/processed/FastSurfer/ |
FastSurfer subject directory (if --fastsurfer) |
Raw / Defaced
| File |
Description |
../../raw/anatMRI/T1/T1_orig.nii.gz |
Original T1 input copy |
../../raw/anatMRI/T1/T1_orig_defaced.nii.gz |
De-faced original T1 (if defacing enabled) |
T2 Outputs (if T2 provided)
| File |
Description |
T2/processed/data/T2.nii.gz |
T2 aligned to T1 native space |
T2/processed/data/T2_brain.nii.gz |
Skull-stripped T2 |
T2/processed/data/T2_unbiased.nii.gz |
Bias-corrected T2 |
T2/processed/data2std/T2_2_std.nii.gz |
T2 in MNI space (linear) |
T2/processed/data2std/T2_2_std_warped.nii.gz |
T2 in MNI space (non-linear) |
T2/preproc/reg/T2_2_std.mat |
T2 → MNI affine |
T2/preproc/lesions/final_mask.nii.gz |
Binary white matter lesion mask (BIANCA) |
T2/preproc/lesions/volume.txt |
Total lesion volume in voxels |
../../raw/anatMRI/T2/T2_orig_defaced.nii.gz |
De-faced original T2 |
Log
| File |
Description |
T1/log/log.txt |
Full processing log with timestamps, parameters, and software versions |