output_organization.sh — Final Output Organisation¶

Location: BRC_structural_pipeline/scripts/output_organization.sh
Authors: Ali-Reza Mohammadi-Nejad, Stamatios N Sotiropoulos
Last updated: 02 Oct 2018

Purpose¶

Moves all intermediate files from temporary working directories into the canonical, human-readable BRC output folder hierarchy. This is the final "tidy-up" step that runs at the end of every successful pipeline execution.

Additionally, when T2 data is present and tissue segmentation is requested, this script runs multi-channel FAST (jointly on T1 and T2 brains) and automatically assigns CSF/GM/WM labels to the output PVE maps.

Operations by Section¶

T1 Data Organisation¶

Moves core T1 volumes from temp/ to processed/data/:

Source	Destination
`temp/T1.nii.gz`	`processed/data/T1.nii.gz`
`temp/T1_brain.nii.gz`	`processed/data/T1_brain.nii.gz`
`temp/T1_brain_mask.nii.gz`	`processed/data/T1_brain_mask.nii.gz`
`temp/T1_unbiased.nii.gz`	`processed/data/T1_unbiased.nii.gz`
`temp/T1_unbiased_brain.nii.gz`	`processed/data/T1_unbiased_brain.nii.gz`
`temp/T1_orig_defaced.nii.gz`	`raw/T1/T1_orig_defaced.nii.gz` (if defacing enabled)

Segmentation Organisation¶

Moves FAST outputs to processed/seg/tissue/sing_chan/ with renamed labels:

Source	Destination
`FAST/T1_brain_pve_0`	`sing_chan/T1_pve_CSF`
`FAST/T1_brain_pve_1`	`sing_chan/T1_pve_GM`
`FAST/T1_brain_pve_2`	`sing_chan/T1_pve_WM`
`FAST/T1_brain_CSF_mask`	`sing_chan/T1_CSF_mask`
`FAST/T1_brain_GM_mask`	`sing_chan/T1_GM_mask`
`FAST/T1_brain_WM_mask`	`sing_chan/T1_WM_mask`
`FAST/T1_brain_pveseg`	`sing_chan/T1_pveseg`
`FAST/T1_brain_seg`	`sing_chan/T1_seg`
`FAST/T1_brain_bias`	`preproc/bias/T1_brain_bias`

Registration Organisation¶

Linear registration files are moved to processed/data2std/ and preproc/reg/:

Source	Destination
`reg/T1_to_MNI_linear`	`data2std/T1_2_std`
`reg/T1_brain_to_MNI_linear`	`data2std/T1_2_std_brain_lin`
`reg/T1_to_MNI_linear.mat`	`preproc/reg/T1_2_std.mat`
Computed inverse	`preproc/reg/std_2_T1.mat`

For RegType 2 or 3, non-linear outputs are also organised:

Source	Destination
`reg/T1_to_MNI_nonlin`	`data2std/T1_2_std_warped`
`reg/T1_brain_to_MNI_nonlin`	`data2std/T1_2_std_brain_warped`
`reg/T1_to_MNI_nonlin_field`	`preproc/reg/T1_2_std_warp_field`
`reg/T1_to_MNI_nonlin_coeff_inv`	`preproc/reg/std_2_T1_warp_field`
`SIENAX/*`	`preproc/SIENAX/`

Multi-Channel Tissue Segmentation (T2 + tissue seg enabled)¶

When both T2 data and --dotissueseg=yes are active, FAST is run in multi-channel mode:

fast -o FAST -g -N -S 2 T1_brain T2_brain

Because FAST does not guarantee a fixed label ordering for multi-channel inputs, the script automatically assigns labels by ranking mean PVE intensities:

# Sort PVE means in ascending order
# Lowest  → CSF
# Middle  → GM
# Highest → WM

This ensures correct labelling regardless of FAST's internal ordering.

Parameters¶

Parameter	Type	Description
`--t1folder`	Path	Root T1 folder
`--t2folder`	Path	Root T2 folder
`--datat1folder`	Path	Destination for processed T1 data
`--data2stdt1folder`	Path	Destination for T1 in standard space
`--segt1folder`	Path	Destination for segmentation outputs
`--regt1folder`	Path	Destination for T1 registration files
`--tempt1folder`	Path	T1 temp folder (source of most files)
`--t2exist`	yes/no	Whether T2 data is present
`--dotissueseg`	yes/no	Whether to run multi-channel FAST
`--dodefacing`	yes/no	Whether de-facing was applied
`--regtype`	1/2/3	Determines which non-linear files to move
`--sienaxt1folder`	Path	SIENAX permanent output folder
`--sienaxtempfolder`	Path	SIENAX temp folder (source)
`--biancat2folder`	Path	BIANCA permanent output folder
`--biancatempfolder`	Path	BIANCA temp folder (source)
`--logfile`	Path	Log file path