Outputs of tedana

tedana derivatives

Filename	Content
t2sv.nii	Limited estimated T2* 3D map. The difference between the limited and full maps is that, for voxels affected by dropout where only one echo contains good data, the full map uses the single echo's value while the limited map has a NaN.
s0v.nii	Limited S0 3D map. The difference between the limited and full maps is that, for voxels affected by dropout where only one echo contains good data, the full map uses the single echo's value while the limited map has a NaN.
ts_OC.nii	Optimally combined time series.
dn_ts_OC.nii	Denoised optimally combined time series. Recommended dataset for analysis.
lowk_ts_OC.nii	Combined time series from rejected components.
midk_ts_OC.nii	Combined time series from "mid-k" rejected components.
hik_ts_OC.nii	High-kappa time series.
comp_table_pca.txt	TEDPCA component table. A tab-delimited file with summary metrics and inclusion/exclusion information for each component from the PCA decomposition.
mepca_mix.1D	Mixing matrix (component time series) from PCA decomposition.
meica_mix.1D	Mixing matrix (component time series) from ICA decomposition. The only differences between this mixing matrix and the one above are that components may be sorted differently and signs of time series may be flipped.
betas_OC.nii	Full ICA coefficient feature set.
betas_hik_OC.nii	High-kappa ICA coefficient feature set
feats_OC2.nii	Z-normalized spatial component maps
comp_table_ica.txt	TEDICA component table. A tab-delimited file with summary metrics and inclusion/exclusion information for each component from the ICA decomposition.

If verbose is set to True:

Filename	Content
t2ss.nii	Voxel-wise T2* estimates using ascending numbers of echoes, starting with 2.
s0vs.nii	Voxel-wise S0 estimates using ascending numbers of echoes, starting with 2.
t2svG.nii	Full T2* map/time series. The difference between the limited and full maps is that, for voxels affected by dropout where only one echo contains good data, the full map uses the single echo's value while the limited map has a NaN. Only used for optimal combination.
s0vG.nii	Full S0 map/time series. Only used for optimal combination.
__meica_mix.1D	Mixing matrix (component time series) from ICA decomposition.
hik_ts_e[echo].nii	High-Kappa time series for echo number echo
midk_ts_e[echo].nii	Mid-Kappa time series for echo number echo
lowk_ts_e[echo].nii	Low-Kappa time series for echo number echo
dn_ts_e[echo].nii	Denoised time series for echo number echo

If gscontrol includes 'gsr':

Filename	Content
T1gs.nii	Spatial global signal
glsig.1D	Time series of global signal from optimally combined data.
tsoc_orig.nii	Optimally combined time series with global signal retained.
tsoc_nogs.nii	Optimally combined time series with global signal removed.

If gscontrol includes 't1c':

Filename	Content
sphis_hik.nii	T1-like effect
hik_ts_OC_T1c.nii	T1 corrected high-kappa time series by regression
dn_ts_OC_T1c.nii	T1 corrected denoised time series
betas_hik_OC_T1c.nii	T1-GS corrected high-kappa components
meica_mix_T1c.1D	T1-GS corrected mixing matrix

Component tables

TEDPCA and TEDICA use tab-delimited tables to track relevant metrics, component classifications, and rationales behind classifications. TEDPCA rationale codes start with a "P", while TEDICA codes start with an "I".

Classification	Description
accepted	BOLD-like components retained in denoised and high-Kappa data
rejected	Non-BOLD components removed from denoised and high-Kappa data
retained	Low-variance components retained in denoised, but not high-Kappa, data

TEDPCA codes

Code	Classification	Description	Algorithm(s)
P001	rejected	Low Rho, Kappa, and variance explained	Kundu decision tree
P002	rejected	Low variance explained	Kundu decision tree
P003	rejected	Kappa equals fmax	Kundu decision tree
P004	rejected	Rho equals fmax	Kundu decision tree
P101	rejected	Cumulative variance explained above 95%	Kundu decision tree (stabilized version)
P102	rejected	Kappa below fmin	Kundu decision tree (stabilized version)
P103	rejected	Rho below fmin	Kundu decision tree (stabilized version)

TEDICA codes

Code	Classification	Description	Algorithm(s)
I001	rejected	Manual exclusion	All
I002	rejected	Rho greater than Kappa or more significant voxels in S0 model than R2 model	Kundu v2.5, Kundu v3.2
I003	rejected	S0 Dice is higher than R2 Dice and high variance explained	Kundu v2.5, Kundu v3.2
I004	rejected	Noise F-value is higher than signal F-value and high variance explained	Kundu v2.5, Kundu v3.2
I005	retained	No good components found	Kundu v2.5
I006	rejected	Mid-Kappa component	Kundu v2.5, Kundu v3.2
I007	retained	Low variance explained	Kundu v2.5
I008	rejected	Artifact candidate type A	Kundu v2.5
I009	rejected	Artifact candidate type B	Kundu v2.5
I010	retained	ign_add0	Kundu v2.5
I011	retained	ign_add1	Kundu v2.5
I101	retained	Miscellaneous artifact	Kundu v3.2
I102	retained	Field artifact	Kundu v3.2
I103	retained	Physiological artifact	Kundu v3.2
I104	retained	Saved at the last second	Kundu v3.2
I105	retained	Orphan component	Kundu v3.2