Raw Data

All of our raw imaging data is stored in a folder called

/[Study-Name]_Imaging/[Study-Name]_BIDS/

Within this folder are subfolders for every subject. All timepoints for a given subject are stored within this folder.

So, for example, all IAM timepoints for subject sub-1002 are stored in the following folders:

/IAM/IAM_Analysis/IAM_BIDS/sub-1002/ses-Y0
/IAM/IAM_Analysis/IAM_BIDS/sub-1002/ses-Y2
/IAM/IAM_Analysis/IAM_BIDS/sub-1002/ses-Y4
/IAM/IAM_Analysis/IAM_BIDS/sub-1002/ses-Y6

Within these ses (session) folders that represent each timepoint for which we have collected data are nifti files organized by type. These types are as follows:

anat (anatomical data; T1w, T2w)
dwi (diffusion data; DKI, FBI
fmri (fmri data; task, resting state)
fmap (field map images)
mrs (spectroscopy data)
pet (pet images)
vista (vista and vista ref images)
other (misc images not to be used in analysis such as head scout files)

Within these folders are images with standard names. BIDS file names always begin with subject ID, followed by session, then file type, then modifiers.

Our standard file names all file names begin with subject ID and session prefixes, eg:

sub-1002_ses-Y0_[sequence]_[modifiers].[extension]

Our standard file name list is as follows:

NOTE: subject ID and session prefixes and file extensions are not present for brevity

anat
    T1w
    T1w_COR
    T1w_TRA
    T2w
    T2w_COR
    T2w_TRA
    T2w_tra_Eq
    T2w_dark-fluid
dwi
    DKI_30dir
    DKI_30dir_TOPUP
    DKI_64dir
    DKI_64dir_TOPUP
    FBI
fmap
    field_map_e1
    field_map_e2
    field_map_e2_ph
    ep2d_sfs
fmri
    Resting_State_1
    Resting_State_2
    Task
mrs
pet
vista
    ViSTa
    ViSTa_REF

Old Filename	New Filename
DKI_30_Dir_i00001	sub-NNN_ses-YY_DKI_30dir
DKI_30_Dir_TOP_UP_PA	sub-NNN_ses-YY_DKI_30dir_TOPUP
DKI_30_Dir	sub-NNN_ses-YY_DKI_30dir
DKI_BIPOLAR_2.5mm_64dir_50slices_TOP_UP_PA	sub-NNN_ses-YY_DKI_64dir_TOPUP
DKI_BIPOLAR_2.5mm_64dir_50slices	sub-NNN_ses-YY_DKI_64dir
DKI_MONOPOLAR_3.0mm_30dir_42slices_topup_i00001	sub-NNN_ses-YY_DKI_30dir_TOPUP
DKI_MONOPOLAR_3.0mm_30dir_42slices	sub-NNN_ses-YY_DKI_30dir
FBI_b6000_128	sub-NNN_ses-YY_FBI
FBI_b8000_256_Siemens	sub-NNN_ses-YY_FBI
gre_field_mapping_e1	sub-NNN_ses-YY_field-map_e1
gre_field_mapping_e2_ph	sub-NNN_ses-YY_field-map_e2ph
gre_field_mapping_e2	sub-NNN_ses-YY_field-map_e2ph
sms3_3.0iso_PA_i00001	sub-NNN_ses-YY_PA
sms3_3.0iso_Resting_State_1	sub-NNN_ses-YY_Resting_1
sms3_3.0iso_Resting_State_2_e1	sub-NNN_ses-YY_Resting_2_e1
sms3_3.0iso_Resting_State_2	sub-NNN_ses-YY_Resting_2
sms3_3.0iso_Task	sub-NNN_ses-YY_Task
t1_mprage_sag_p2_iso_MPR_Cor	sub-NNN_ses-YY_T1w_Cor
t1_mprage_sag_p2_iso_MPR_Tra	sub-NNN_ses-YY_T1w_Tra
t1_mprage_sag_p2_iso	sub-NNN_ses-YY_T1w
t2_tse_dark-fluid_tra	sub-NNN_ses-YY_T2w_tra
t2_tse_dark-fluid_traa	sub-NNN_ses-YY_T2w_traa
TDE_ep2d_diff_brad300_off_e1	sub-NNN_ses-YY_TDE_off
TDE_ep2d_diff_brad300	sub-NNN_ses-YY_TDE
ViSTa_2.0mm	sub-NNN_ses-YY_ViSTa
ViSTa_2.0mma	sub-NNN_ses-YY_ViSTaa
ViSTa_REF_2.0mm_FA28	sub-NNN_ses-YY_ViSTa_REF