Get list of participants, explore folders and count files using the function scout_bids_for_gui_env
To feed the GUI_environments you need a list of participants. This list can be generated using the function scout_bids_for_gui_env. This function will allow you to:
- Get a properly formatted list to feed the GUI_environments.
- Make a report of dtseries, ptseries and dot mat files.
- Generate a report of folders with missing data.
This is a basic example of how to run it:
root_path='C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human';
[T_count, list,text_counts,text_missing] = scout_bids_for_gui_env(root_path);
Mandatory Input
root_path is the path to the derivatives folder containing the subjetc ids
Outputs
T_count.Table reporting the file types per participant in theroot_path.
| list_func | rest_star_mat | rest_bold_dtseries_nii_ |
|---|---|---|
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_01\fake_visit_1\func | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_02\fake_visit_1\func | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_03\fake_visit_1\func | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_04\fake_visit_1\func | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_05\fake_visit_1\func | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_06\fake_visit_1\func | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_07\fake_visit_1\func | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_08\fake_visit_1\func | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_09\fake_visit_1\func | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_10\fake_visit_1\func | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_11\fake_visit_1\func | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_12\fake_visit_1\func | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_13\fake_visit_1\func | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_14\fake_visit_1\func | 1 | 1 |
listA matlab cell with the fullpath of subjects with data. This cell has the same content as the txt file that is created ans saved by this function.
| list |
|---|
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_01\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_02\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_03\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_04\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_05\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_06\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_07\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_08\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_09\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_10\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_11\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_12\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_13\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_14\fake_visit_1 |
text_counts. Cell array showing a summary count of file per type/extension.
| text_counts |
|---|
| N func = 14 |
| N *rest*.mat = 14 |
| N *rest*bold*dtseries.nii* = 14 |
text_missing. Cell array showing a summary count of missing files per type/extension.
| text_missing |
|---|
| N folders with missing *rest*.mat data = 0 |
| N folders with missing *rest*bold*dtseries.nii* data = 0 |
- txt file. It also save a txt file indicating the number of participants with data to calculate connectivity matrices. The default name is
list.txt.
Finding subjects with specific parcellations schemas
To look for paths with several parcellation schemas, for example Gordon and HCP, you can use the extra argument extra_strings_to_match as follows:
extra_strings_to_match{1}='\*rest\*bold\*ordon*ptseries.nii*';
extra_strings_to_match{2}='\*rest\*bold\*HCP*ptseries.nii*';
[T_count, list,text_counts,text_missing] = scout_bids_for_gui_env(path_BIDS_data,...
'extra_strings_to_match',extra_strings_to_match)
Corresponding outputs are:
T_count.Table reporting the file types per participant in theroot_path.
| list_func | rest_star_mat | rest_bold_dtseries_nii_ | rest_bold_ordon_ptseries_nii_ | rest_bold_HCP_ptseries_nii_ |
|---|---|---|---|---|
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_01\fake_visit_1\func | 1 | 1 | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_02\fake_visit_1\func | 1 | 1 | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_03\fake_visit_1\func | 1 | 1 | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_04\fake_visit_1\func | 1 | 1 | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_05\fake_visit_1\func | 1 | 1 | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_06\fake_visit_1\func | 1 | 1 | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_07\fake_visit_1\func | 1 | 1 | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_08\fake_visit_1\func | 1 | 1 | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_09\fake_visit_1\func | 1 | 1 | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_10\fake_visit_1\func | 1 | 1 | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_11\fake_visit_1\func | 1 | 1 | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_12\fake_visit_1\func | 1 | 1 | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_13\fake_visit_1\func | 1 | 1 | 1 | 1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_14\fake_visit_1\func | 1 | 1 | 1 | 1 |
listA matlab cell with the fullpath of subjects with data. This cell has the same content as the txt file that is created ans saved by this function.
| list |
|---|
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_01\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_02\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_03\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_04\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_05\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_06\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_07\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_08\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_09\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_10\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_11\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_12\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_13\fake_visit_1 |
| C:\Users\oscar\OneDrive\matlab_code\GUI_environments\data\anonymized_human\fake_ID_14\fake_visit_1 |
text_counts. Cell array showing a summary count of file per type/extension.
| text_counts |
|---|
| N func = 14 |
| N *rest*.mat = 14 |
| N *rest*bold*dtseries.nii* = 14 |
| N *rest*bold*ordon*ptseries.nii* = 14 |
| N *rest*bold*HCP*ptseries.nii* = 14 |
text_missing. Cell array showing a summary count of missing files per type/extension.
| text_missing |
|---|
| N folders with missing *rest*.mat data = 0 |
| N folders with missing *rest*bold*dtseries.nii* data = 0 |
| N folders with missing *rest*bold*ordon*ptseries.nii* data = 0 |
| N folders with missing *rest*bold*HCP*ptseries.nii* data = 0 |
- txt file. It also save a txt file indicating the number of participants with data to calculate connectivity matrices.
Specifying preffix for output txt file
To add a preffix to the txt file made by scout_bids_for_gui_env, provide the optional argument preffix:
preffix='only_Gordon';
[T_count, list,text_counts,text_missing] = scout_bids_for_gui_env(path_BIDS_data,...
'preffix',preffix)
Avoiding dtseries
If for some reason you only need a list of participants with parcellaterd data (i.e., you do not need/have dtseries), set the additional argument exclude_dtseries_flag equal to 1:
exclude_dtseries_flag=1;
[T_count, list,text_counts,text_missing] = scout_bids_for_gui_env(path_BIDS_data,...
'extra_strings_to_match',extra_strings_to_match,...
'exclude_dtseries_flag',exclude_dtseries_flag,...
Example using several optional arguments
preffix='only_HCP_no_dtseries';
exclude_dtseries_flag=1;
extra_strings_to_match='*rest*bold*HCP*ptseries.nii*';
[T_count, list,text_counts,text_missing] = scout_bids_for_gui_env(path_BIDS_data,...
'extra_strings_to_match',extra_strings_to_match,...
'exclude_dtseries_flag',exclude_dtseries_flag,...
'extra_strings_to_match',extra_strings_to_match)