T1 Files and fields

preproc_folder

U:\HCPpre\T1preprocess\CONTROL\HCP100307\

initnativefolder_study

U:\HCPpre\T1preprocess\CONTROL\HCP100307\T1_initnative_1series\

t1_im

all T1 images

{'U:\HCPpre\T1preprocess\CONTROL\HCP100307\T1w_MPR1E1003070120150127S1\E1003070120150127S01I01.nii'}

t1_native_old
(used to be “t1_native”)

image in native space, with native bounding box and voxel size

U:\HCPpre\T1preprocess\CONTROL\HCP100307\T1_initnative_1series\E1003070120150127S01I01.nii

t1_native
(used to be “t1_base”)

image in native space (same as t1_native_old for 2021 onwards)

U:\HCPpre\T1preprocess\CONTROL\HCP100307\T1_initnative_1series\E1003070120150127S01I01.nii

t1
(reference for native space)

resliced T1 in native space with fixed bounding box and voxel size

U:\HCPpre\T1preprocess\CONTROL\HCP100307\T1_ref_vox0.75_bb_min_-90_-126_-72_max_90_90_108\rE1003070120150127S01I01.nii

t1_corr

corrected for bias

[not implemented yet]

[same folder as “t1”] …\mri\mirE1003070120150127S01I01.nii

t1_gm

[same folder as “t1”] …\c1rE1003070120150127S01I01.nii

[same folder as “t1”] …\mri\p1rE1003070120150127S01I01.nii

t1_wm

…\c2rE1003070120150127S01I01.nii

…\mri\p2rE1003070120150127S01I01.nii

t1_csf

…\c3rE1003070120150127S01I01.nii

…\mri\p3rE1003070120150127S01I01.nii

t1_whhc

white matter hyperintensities

…\mri\p7rE1003070120150127S01I01.nii

t1_rc

5 images (cell array)

…\rc1rE1003070120150127S01I01.nii

…\rc2rE1003070120150127S01I01.nii

…\rc3rE1003070120150127S01I01.nii

…\rc4rE1003070120150127S01I01.nii

…\rc5rE1003070120150127S01I01.nii

t1_seg

segmentation (what is this? not sure)

…\rE1003070120150127S01I01_seg.mat

t1_darteldeffield

deformation field (3-volume nifti)
e.g., DARTEL native to template

u_…nii

t1_shootflowfield

flow field (3-volume nifti) e.g., calculated in CAT12

y_…nii

t1_brainsurf_native

brain surface in native space

_surf.gii

t1_brainrender_native

rendering (old way of showing blobs on surface)

render_….mat

t1_brainprob_native, t1_grayprob_native, t1_whiteprob_native, t1_csfprob_native

probability maps

brain = gm + wm

t1_brainmask_native, t1_graymask_native, t1_whitemask_native, t1_csfmask_native

masks (prob > 0.5)
brain = gm+wm > 0.5

brainmask_….nii, graymask_….nii, whitemask….nii, csfmask….nii

totalvol_brain, totalvol_gm, totalvol_wm, totalvol_csf, totalvol_tiv

volumes (mm^3)

no files; calculated from probability files

totalvol_graywhite_ratio, totalvol_braincsf_ratio, totalvol_braintiv_ratio

ratios

based on volumes

t1_jacobian

jacobian

jac_….nii

t1_jacobian_norm

normalized jacobian

…\mri\wj_rE1003070120150127S01I01.nii

t1_norm, t1_gm_norm, t1_wm_norm, t1_csf_norm

normalized

w….nii

…\mri\wmi…rE1003070120150127S01I01.nii

…\mri\wp…rE1003070120150127S01I01.nii

etc.