# 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:

{% code overflow="wrap" %}

```
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
```

{% endcode %}

<table><thead><tr><th width="245.5">Old Filename</th><th width="433.5">New Filename</th></tr></thead><tbody><tr><td>DKI_30_Dir_i00001</td><td>sub-NNN_ses-YY_DKI_30dir</td></tr><tr><td>DKI_30_Dir_TOP_UP_PA</td><td>sub-NNN_ses-YY_DKI_30dir_TOPUP</td></tr><tr><td>DKI_30_Dir</td><td>sub-NNN_ses-YY_DKI_30dir</td></tr><tr><td>DKI_BIPOLAR_2.5mm_64dir_50slices_TOP_UP_PA</td><td>sub-NNN_ses-YY_DKI_64dir_TOPUP</td></tr><tr><td>DKI_BIPOLAR_2.5mm_64dir_50slices</td><td>sub-NNN_ses-YY_DKI_64dir</td></tr><tr><td>DKI_MONOPOLAR_3.0mm_30dir_42slices_topup_i00001</td><td>sub-NNN_ses-YY_DKI_30dir_TOPUP</td></tr><tr><td>DKI_MONOPOLAR_3.0mm_30dir_42slices</td><td>sub-NNN_ses-YY_DKI_30dir</td></tr><tr><td>FBI_b6000_128</td><td>sub-NNN_ses-YY_FBI</td></tr><tr><td>FBI_b8000_256_Siemens</td><td>sub-NNN_ses-YY_FBI</td></tr><tr><td>gre_field_mapping_e1</td><td>sub-NNN_ses-YY_field-map_e1</td></tr><tr><td>gre_field_mapping_e2_ph</td><td>sub-NNN_ses-YY_field-map_e2ph</td></tr><tr><td>gre_field_mapping_e2</td><td>sub-NNN_ses-YY_field-map_e2ph</td></tr><tr><td>sms3_3.0iso_PA_i00001</td><td>sub-NNN_ses-YY_PA</td></tr><tr><td>sms3_3.0iso_Resting_State_1</td><td>sub-NNN_ses-YY_Resting_1</td></tr><tr><td>sms3_3.0iso_Resting_State_2_e1</td><td>sub-NNN_ses-YY_Resting_2_e1</td></tr><tr><td>sms3_3.0iso_Resting_State_2</td><td>sub-NNN_ses-YY_Resting_2</td></tr><tr><td>sms3_3.0iso_Task</td><td>sub-NNN_ses-YY_Task</td></tr><tr><td>t1_mprage_sag_p2_iso_MPR_Cor</td><td>sub-NNN_ses-YY_T1w_Cor</td></tr><tr><td>t1_mprage_sag_p2_iso_MPR_Tra</td><td>sub-NNN_ses-YY_T1w_Tra</td></tr><tr><td>t1_mprage_sag_p2_iso</td><td>sub-NNN_ses-YY_T1w</td></tr><tr><td>t2_tse_dark-fluid_tra</td><td>sub-NNN_ses-YY_T2w_tra</td></tr><tr><td>t2_tse_dark-fluid_traa</td><td>sub-NNN_ses-YY_T2w_traa</td></tr><tr><td>TDE_ep2d_diff_brad300_off_e1</td><td>sub-NNN_ses-YY_TDE_off</td></tr><tr><td>TDE_ep2d_diff_brad300</td><td>sub-NNN_ses-YY_TDE</td></tr><tr><td>ViSTa_2.0mm</td><td>sub-NNN_ses-YY_ViSTa</td></tr><tr><td>ViSTa_2.0mma</td><td>sub-NNN_ses-YY_ViSTaa</td></tr><tr><td>ViSTa_REF_2.0mm_FA28</td><td>sub-NNN_ses-YY_ViSTa_REF</td></tr></tbody></table>


---

# Agent Instructions: Querying This Documentation

If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.

Perform an HTTP GET request on the current page URL with the `ask` query parameter:

```
GET https://bridge-lab.gitbook.io/docs/imaging/data-organization/general-documentation/bids-data-organization/raw-data.md?ask=<question>
```

The question should be specific, self-contained, and written in natural language.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.

Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.