PitchToBids

Goal: take the PITCH dataset and rename/move files so they conform to the BIDS standard

Getting Started, Step 0

1. clone this repository: click on the green clone/download button and select the copy to clipboard option
2. On your linux computer, open a terminal and type git clone https://github.com/Mentee-Assignments/PitchToBids/
3. cd into your newly cloned repository

after you make a change

1. say you added a txt file called "file.txt" in the top level directory (e.g. PitchToBids/file.txt)
2. add the file to be tracked by git using git add file.txt (assuming you are in the PitchToBids directory)
3. commit the file by typing git commit -m 'added file.txt'
4. then submit the change to the online repository by typing git push origin master

Step 1: Come up with a template for naming the 4 files (anat, rest, flanker, asl)

• Guides:
  • BIDS spec
  • BIDS paper
  • BIDS ASL spec
• Result:
  • Template for each filetype (anat, rest, flanker, asl)
    • ex: sub-[0-9]+/ses-[ExercisePre,ExcercisePost]/anat/TEMPLATE-FILENAME
  • Place the templates as a .txt file in this respository

Step 2: Coding

• Background: REGEX
  • Excellent Introduction
    • matching tutorial exercises
    • ^^^ This will be crucial to matching the files we want to change and "grabbing" them intelligently

Step 3: Describe the behavioral data for the flanker task

• Reading section 4.2 of the BIDS spec gives us the general format of the output behavioral tsv we want. A simple end result will look like this:

onset	duration	response_time	correct	trial_type
8.00	0.517	0.909	1	congruent
12.00	0.517	1.217	0	incongruent
22.00	0.517	0.833	1	congruent
30.00	0.517	1.011	1	incongruent

• The files that contain all the pertinent information look like this:
  • P01C1BOL_ALL_Incorrect_A_Duration.txt
  • P01C1BOL_Congruent_Correct_A_Duration.txt
  • P01C1BOL_Congruent_Correct_A_RT.txt
  • P01C1BOL_Congruent_Incorrect_A_Duration.txt
  • P01C1BOL_Congruent_Incorrect_A_RT.txt
  • P01C1BOL_Incongruent_Correct_A_Duration.txt
  • P01C1BOL_Incongruent_Correct_A_RT.txt
  • P01C1BOL_Incongruent_Incorrect_A_Duration.txt
  • P01C1BOL_Incongruent_Incorrect_A_RT.txt
  • P01C1BOL_Neutral_Correct_A_Duration.txt
  • P01C1BOL_Neutral_Correct_A_RT.txt
  • P01C1BOL_Neutral_Incorrect_A_Duration.txt
  • P01C1BOL_Neutral_Incorrect_A_RT.txt
• From that listing we see we will get the "correct" information and the "trial_type" information from the filenames.
• The contents of a Duration file look like this:

10.009059	0.51663	1
23.957940	0.51662	1
45.906190	0.51662	1
55.888724	0.51662	1
57.871890	0.51662	1
65.854588	0.51662	1
105.751380	0.51662	1
109.717748	0.51660	1
121.666754	0.51662	1
129.649453	0.51663	1
147.598022	0.51662	1
153.580874	0.51662	1
177.845593	0.51662	1
201.743675	0.51662	1
217.659050	0.51663	1
241.607136	0.51662	1
297.402644	0.51663	1
307.368512	0.51663	1
323.317242	0.51662	1
327.300254	0.51662	1
335.282948	0.51662	1

• ^^ The first column corresponds to onset, the second column to duration, and we don't care about the third column.

• The contents of a RT file look like this:

10.009059	0.50260	1
23.957940	0.52935	1
45.906190	0.63653	1
55.888724	0.60575	1
57.871890	0.82254	1
65.854588	0.72759	1
105.751380	0.67776	1
109.717748	0.63933	1
121.666754	0.72197	1
129.649453	1.14706	1
147.598022	0.76601	1
153.580874	0.68698	1
177.845593	0.71768	1
201.743675	0.93095	1
217.659050	0.93515	1
241.607136	0.51674	1
297.402644	0.90944	1
307.368512	0.79132	1
323.317242	0.91417	1
327.300254	0.99504	1
335.282948	0.89215	1

• ^^ The first column corresponds to onset, the second column to response_time, and the third we don't care about.

• Finally the name of the file will conform to section 8.5 of the BIDS spec. The output file name will be identical to the flanker bold file name, except the suffix will change from _bold.nii.gz to _events.tsv.

• From this we have all the information we need to create a BIDS behavioral tsv.

Step 4: Write out how you would solve this problem in English

• first think of the general steps required to solve this problem and then think about how you would complete each of those steps. This will determine the outline of the code solution.

Step 5: Implement the solution in python