move_rename.sh — Legacy Output Reorganisation¶

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

Legacy Script

This script is designed for the legacy fsl_anat-based preprocessing path (FSL_anat.sh → move_rename.sh). The current default path uses run_T1_preprocessing.sh → output_organization.sh. See Difference from output_organization.sh below.

Purpose¶

Moves and renames files from the <T1Folder>/<anatFolder>/ directory structure produced by FSL_anat.sh into the canonical BRC folder hierarchy. When T2 data is present, it also co-registers the T2 to the T1 using epi_reg (for better white-matter-boundary alignment), optionally runs multi-channel FAST, and computes the full T2→MNI warp.

Operations¶

T1 Data¶

Source (`<anatFolder>/`)	Destination
`T1_biascorr`	`processed/data/T1`
`T1_biascorr_brain`	`processed/data/T1_brain`
`T1_biascorr_brain_mask`	`processed/data/T1_brain_mask`
`T1_fast_pve_0`	`seg/tissue/sing_chan/T1_pve_CSF`
`T1_fast_pve_1`	`seg/tissue/sing_chan/T1_pve_GM`
`T1_fast_pve_2`	`seg/tissue/sing_chan/T1_pve_WM`
`T1_fast_pveseg`	`seg/tissue/sing_chan/T1_pveseg`
`T1_fast_seg`	`seg/tissue/sing_chan/T1_seg`
`T1_to_MNI_linear`	`processed/data2std/T1_2_std`
`T1_to_MNI_linear_temp.mat`	`preproc/reg/T1_2_std.mat`
`T1_to_MNI_nonlin`	`processed/data2std/T1_2_std_warp`
`T1_to_MNI_nonlin_coeff`	`preproc/reg/T1_2_std_warp_coeff`
`T1_to_MNI_nonlin_field`	`preproc/reg/T1_2_std_warp_field`
`T1_to_MNI_nonlin_jac`	`preproc/reg/T1_2_std_warp_jac`
`MNI_to_T1_nonlin_field`	`preproc/reg/std_2_T1_warp_field`

Subcortical Structures (if `--dosubseg=yes`)¶

FIRST shape files (.bvars and .vtk) for the following structures are moved to seg/sub/shape/:

Accumbens (L/R), Amygdala (L/R), Caudate (L/R), Hippocampus (L/R), Pallidum (L/R), Putamen (L/R), Thalamus (L/R), Brainstem.

T2 Co-registration and Organisation (if T2 present)¶

T2→T1 co-registration uses epi_reg (boundary-based registration) for improved accuracy at the white matter boundary:

epi_reg \
    --epi=T2_brain \
    --t1=T1 \
    --t1brain=T1_brain \
    --out=reg/T2_2_T1_init \
    --wmseg=sing_chan/T1_pve_thr_WM

flirt -in T2_brain -ref T1_brain \
      -init T2_2_T1_init.mat \
      -out reg/T2_2_T1 -omat reg/T2_2_T1.mat -dof 6

If multi-channel segmentation is run, epi_reg is re-run using the multi-channel WM mask for improved alignment, and the T2→MNI non-linear warp is produced via:

applywarp --rel \
    --in=T2 \
    --ref=MNI152_T1_1mm \
    --premat=T2_2_T1.mat \
    --warp=T1_2_std_warp_coeff \
    --out=data2std/T2_to_std_warp

Parameters¶

Parameter	Type	Description
`--t1folder`	Path	Root T1 folder
`--t2folder`	Path	Root T2 folder
`--t2exist`	yes/no	Whether T2 data is present
`--dosubseg`	yes/no	Whether subcortical segmentation was run
`--dotissueseg`	yes/no	Whether to run multi-channel FAST
`--anatname`	String	Name of the `fsl_anat` output directory within T1/T2 folder
`--datat1folder`	Path	Destination for processed T1 data
`--data2stdt1folder`	Path	Destination for T1 in standard space
`--segt1folder`	Path	Destination for T1 segmentation outputs
`--regt1folder`	Path	Destination for T1 registration files
`--tempt1folder`	Path	T1 temp folder
`--datat2folder`	Path	Destination for processed T2 data
`--data2stdt2folder`	Path	Destination for T2 in standard space
`--regt2folder`	Path	Destination for T2 registration files
`--tempt2folder`	Path	T2 temp folder
`--logfile`	Path	Log file path

Difference from output_organization.sh¶

Aspect	`move_rename.sh`	`output_organization.sh`
Preprocessing path	Legacy: `FSL_anat.sh`	Current: `run_T1_preprocessing.sh`
Input naming	`T1_biascorr`	`T1_unbiased`
T2→T1 co-reg	`epi_reg` (boundary-based)	T1 brain mask applied directly
Subcortical	Moves FIRST `.bvars`/`.vtk` to `shape/`	Subcortical support removed (commented)
FSLanat temp	Copies residual `fsl_anat` files to `FSLanat/`	No such copy