From 129b6539b839b7f107f8bcfc00045fad6f1d3521 Mon Sep 17 00:00:00 2001 From: Aaronearlerichardson Date: Mon, 12 Feb 2024 16:06:17 -0500 Subject: [PATCH] fixed headings --- docs/BIDS_converter.rst | 3 +- docs/GlobalLocal/index.rst | 484 +++++++++++++++++++------------------ 2 files changed, 246 insertions(+), 241 deletions(-) diff --git a/docs/BIDS_converter.rst b/docs/BIDS_converter.rst index d5cc251..9b84db2 100644 --- a/docs/BIDS_converter.rst +++ b/docs/BIDS_converter.rst @@ -8,8 +8,7 @@ Data2BIDS :module: BIDS_converter.data2bids :func: get_parser -Tasks ------ + Each task has its own specific needs, and therefore has extending guides. Each task has it's own branch on github. .. toctree:: diff --git a/docs/GlobalLocal/index.rst b/docs/GlobalLocal/index.rst index 0a63846..50b0988 100644 --- a/docs/GlobalLocal/index.rst +++ b/docs/GlobalLocal/index.rst @@ -1,312 +1,318 @@ Global Local ============ -Preprocessing Guide -------------------- ecog_preprocessing (Mat) → makeTrials_GL (Mat) → BIDS_coding (WSL) -* **Step 1: Download data files (Box)** - - #. **Go to Box → ECoG_Task_Data → Cogan_Task_Data** and locate the - *Subject (D#) folder → Global Local task folder → All blocks* - subfolder - #. **Download** **all** **Box** **data files from “All Blocks”** folder - #. Then **Copy + Paste** files into **Local PC** folder in - **CoganLabNL** → **InUnit Preprocessing** → **Subject (D#) → Global - Local → All blocks** - #. **KEY**: locate the Excel csv file titled: - ``GL_MainTask_Data_D#_taskdate`` - #. **RENAME this file to** ``Trials`` - #. **EDF file** : - *2 options - Download (local PC) or Box Drive (no download)* - #. **Download** : from **TaskUploadDir** - **Box → TaskUploadDir → Download** → move to same local PC Global Local folder (Only if you want to download!) - - #. **Box Drive** : No download, will use Box Drive path in ``edf_filename`` - variable instead of local PC path → **See Step 2!** - -* **Step 2: ecog_preprocessing(Matlab)** - *general preprocessing script* - - #. Once your files are downloaded and Trials is renamed, open Matlab - and run the **ecog_preprocessing** script *(used for all tasks preprocessing)* - #. Start the same as all other tasks → create a new ``Case`` for the - task (Global Local = **009** ), - #. Fill in all of the case variable information accordingly: **see differences!** - - #. **KEY 1** - for **Global Local only**, - the ``ptb_trialInfo`` is commented out! → put a ``%`` - (percentage sign) in front! This is because we do not need - to get trialInfo – it is replaced by the **Trials** excel sheet we - renamed in Step 1. - #. **KEY 2** - ``edf_filename`` variable (path) will - change depending on if you downloaded the EDF above from Box, or if - you are uploading it directly from Box Drive: - #. **Downloaded EDF** path to InUnit Preprocessing (PC): ``C:\Users\ncl24\Desktop\CoganLabNL\InUnit Preprocessing\D81\Lexical Delay\D# DATE COGAN_TASKNAME.EDF`` - #. **Box Drive EDF** path to TaskUploadDir (Box): ``C:\Users\ncl24\Box\CoganLab\ECoG_Task_Data\TaskUploadDir\D# DATE COGAN_TASKNAME.EDF`` - - #. Once all variables are filled out, **highlight + run (F9)** to load - into your workspace - #. Ignore the trialInfo section (don’t need trialInfo) → Go straight to - the **edfread + labels** section & run! - #. This will read the EDF file to create your ``labels`` variable - #. Then, run the following **extract trigger + mic channel** section - #. This will create your ``trigger`` & ``mic`` variables, as well as - save them as ``trigger.mat`` & ``mic.mat`` files in your task - folder. - #. Finally, run the **.ieeg.dat + experiment** file section, that will - save the ``experiment.mat`` & ``.ieeg.dat`` files in your task - folder - #. As well as create the folders **mat** & **taskdate** *(e.g.**230807**)* - - #. Move the **experiment** file into the **mat** folder - #. At the end of Step 5, the **Trials.mat** file will automatically save under the **taskdate (230807) → mat** folder on Box! - -* **Step 3: MaketrigTimes (Matlab)** - *trigTimes + trigTimes_audioAligned files* - - #. When you reach the **maketrigtimes** section, you will open the - ``maketrigtimes.m`` script and run it in a separate window next to - ecog_preprocessing. - #. *In order to run maketrigtimes successfully, you will need to have*: - - #. The **trigger** variable already loaded in your workspace - * Should already be there if going straight from running ecog_preprocessing – - but if not, double-click on trigger saved in folder - #. Already run ``edfread_fast`` - - * If not, go back and run this in ecog_preprocessing & make sure that your ``edf_filename`` variable (path - to EDF) from the case variables is loaded in your workspace before - doing so. - #. Run the first section at the top to load the graph of the triggers - - * **Uncomment the -triggers (negative) linefor Global Local!** - - * Otherwise the graph will appear upside down - #. Then, proceed as usual and make the trigTimes adjustments you do for - all other tasks +Step 1: Download data files (Box) +--------------------------------- + +#. **Go to Box → ECoG_Task_Data → Cogan_Task_Data** and locate the + *Subject (D#) folder → Global Local task folder → All blocks* + subfolder +#. **Download** **all** **Box** **data files from “All Blocks”** folder +#. Then **Copy + Paste** files into **Local PC** folder in + **CoganLabNL** → **InUnit Preprocessing** → **Subject (D#) → Global + Local → All blocks** +#. **KEY**: locate the Excel csv file titled: + ``GL_MainTask_Data_D#_taskdate`` +#. **RENAME this file to** ``Trials`` +#. **EDF file** : + *2 options - Download (local PC) or Box Drive (no download)* + #. **Download** : from **TaskUploadDir** + **Box → TaskUploadDir → Download** → move to same local PC Global Local folder (Only if you want to download!) + + #. **Box Drive** : No download, will use Box Drive path in ``edf_filename`` + variable instead of local PC path → **See Step 2!** + +Step 2: ecog_preprocessing(Matlab) +---------------------------------- +*general preprocessing script* + +#. Once your files are downloaded and Trials is renamed, open Matlab + and run the **ecog_preprocessing** script *(used for all tasks preprocessing)* +#. Start the same as all other tasks → create a new ``Case`` for the + task (Global Local = **009** ), +#. Fill in all of the case variable information accordingly: **see differences!** + + #. **KEY 1** - for **Global Local only**, + the ``ptb_trialInfo`` is commented out! → put a ``%`` + (percentage sign) in front! This is because we do not need + to get trialInfo – it is replaced by the **Trials** excel sheet we + renamed in Step 1. + #. **KEY 2** - ``edf_filename`` variable (path) will + change depending on if you downloaded the EDF above from Box, or if + you are uploading it directly from Box Drive: + #. **Downloaded EDF** path to InUnit Preprocessing (PC): ``C:\Users\ncl24\Desktop\CoganLabNL\InUnit Preprocessing\D81\Lexical Delay\D# DATE COGAN_TASKNAME.EDF`` + #. **Box Drive EDF** path to TaskUploadDir (Box): ``C:\Users\ncl24\Box\CoganLab\ECoG_Task_Data\TaskUploadDir\D# DATE COGAN_TASKNAME.EDF`` + +#. Once all variables are filled out, **highlight + run (F9)** to load + into your workspace +#. Ignore the trialInfo section (don’t need trialInfo) → Go straight to + the **edfread + labels** section & run! +#. This will read the EDF file to create your ``labels`` variable +#. Then, run the following **extract trigger + mic channel** section +#. This will create your ``trigger`` & ``mic`` variables, as well as + save them as ``trigger.mat`` & ``mic.mat`` files in your task + folder. +#. Finally, run the **.ieeg.dat + experiment** file section, that will + save the ``experiment.mat`` & ``.ieeg.dat`` files in your task + folder +#. As well as create the folders **mat** & **taskdate** *(e.g.**230807**)* + + #. Move the **experiment** file into the **mat** folder + #. At the end of Step 5, the **Trials.mat** file will automatically save under the **taskdate (230807) → mat** folder on Box! + +Step 3: MaketrigTimes (Matlab) +------------------------------- +*trigTimes + trigTimes_audioAligned files* + +#. When you reach the **maketrigtimes** section, you will open the + ``maketrigtimes.m`` script and run it in a separate window next to + ecog_preprocessing. +#. *In order to run maketrigtimes successfully, you will need to have*: + + #. The **trigger** variable already loaded in your workspace + * Should already be there if going straight from running ecog_preprocessing – + but if not, double-click on trigger saved in folder + #. Already run ``edfread_fast`` + + * If not, go back and run this in ecog_preprocessing & make sure that your ``edf_filename`` variable (path + to EDF) from the case variables is loaded in your workspace before + doing so. +#. Run the first section at the top to load the graph of the triggers + + * **Uncomment the -triggers (negative) linefor Global Local!** + + * Otherwise the graph will appear upside down +#. Then, proceed as usual and make the trigTimes adjustments you do for + all other tasks + + #. **Global Local-specific Task Info** : + + #. Total # triggers → **trigTimes** = **448** + #. **4 blocks** total, **112** triggers per block + + #. *Rare cases could have 512 total trigs, 128 per block* + + #. Seconds between triggers = **1.5** + #. Threshold (thresh) = **-1.25** - #. **Global Local-specific Task Info** : + #. Bc graph is inverted / negative from the -triggers line! - #. Total # triggers → **trigTimes** = **448** - #. **4 blocks** total, **112** triggers per block + #. If you need to delete excess triggers (first, last, random in + middle) run: ``trigTimes([1,2,3,etc.]) = []`` - #. *Rare cases could have 512 total trigs, 128 per block* + * *Fill in brackets with which specific trigger numbers you need to delete!* + #. Once ``trigTimes = 448``, run the final section to save + ``trigTimes.mat`` file to your PC folder! +#. Finally, return to the **ecog_preprocessing** script tab and run the + section below, to align the audio to your saved trigTimes - #. Seconds between triggers = **1.5** - #. Threshold (thresh) = **-1.25** + * This will create the ``trigTimes_audioAligned.mat`` file and save it + into your PC folder - #. Bc graph is inverted / negative from the -triggers line! +Step 4: Upload Files + Copy EDF to Box D_Data +--------------------------------------------- - #. If you need to delete excess triggers (first, last, random in - middle) run: ``trigTimes([1,2,3,etc.]) = []`` +#. **Before moving on! → Upload all files to Box** → **D_Data** from InUnit Preprocessing folder: **Box → D_Data → Global Local → Subject (D#)** - * *Fill in brackets with which specific trigger numbers you need to delete!* - #. Once ``trigTimes = 448``, run the final section to save - ``trigTimes.mat`` file to your PC folder! - #. Finally, return to the **ecog_preprocessing** script tab and run the - section below, to align the audio to your saved trigTimes - * This will create the ``trigTimes_audioAligned.mat`` file and save it - into your PC folder + #. Critical because the **makeTrials_GL script pulls and uses files from Box only! (D_Data Global Local folder specifically)** -* **Step 4: Upload Files + Copy EDF to Box D_Data** + * So before running that script, all files must be uploaded there in order for it to work + #. Upload the files to D_Data in the exact same way as all other tasks! - only difference = Trials.csv instead of trialInfo +#. **Also! → Copy EDF file into D_Data folder from TaskUploadDir** + #. The edfread command in this program can only read EDFs / files from + the D_Data folder!!! + #. So you must Copy the EDF from TaskUploadDir into the D_Data folder + with the rest of the uploaded files! + #. SEE BELOW - you must also change Path to EDF!!! + * Of ``edf_filename`` variable + ``edfread_fast(edf_filename)`` commands! - #. **Before moving on! → Upload all files to Box** → **D_Data** from InUnit Preprocessing folder: **Box → D_Data → Global Local → Subject (D#)** +Step 5: makeTrials_GL (Matlab) +------------------------------ +*Global Local only script to make Trials.mat* - #. Critical because the **makeTrials_GL script pulls and uses files from Box only! (D_Data Global Local folder specifically)** +#. Once all files have been uploaded to **Box → D_Data** folder, return + to Matlab and run the ``makeTrials_GL.m`` script in another separate + tab window → this script will output the final ``Trials.mat`` file + when finished! +#. **STEPS TO RUN SUCCESSFULLY** *(also written on script!)* - * So before running that script, all files must be uploaded there in order for it to work - #. Upload the files to D_Data in the exact same way as all other tasks! - only difference = Trials.csv instead of trialInfo - #. **Also! → Copy EDF file into D_Data folder from TaskUploadDir** - #. The edfread command in this program can only read EDFs / files from - the D_Data folder!!! - #. So you must Copy the EDF from TaskUploadDir into the D_Data folder - with the rest of the uploaded files! - #. SEE BELOW - you must also change Path to EDF!!! - * Of ``edf_filename`` variable + ``edfread_fast(edf_filename)`` commands! + * **Step 1** : **Copy EDF file into D_Data Box folder!** (from TaskUploadDir) -* **Step 5: makeTrials_GL (Matlab)** - *Global Local only script to make Trials.mat* + * **KEY** - Make sure EDF file is copied into the **D_Data** Subject Global Local folder on Box! + * **Step 2**: **Edit info** (specific to each subject) + **copy in command line to run each command below (A, B, C) ONE AT A TIME:** - #. Once all files have been uploaded to **Box → D_Data** folder, return - to Matlab and run the ``makeTrials_GL.m`` script in another separate - tab window → this script will output the final ``Trials.mat`` file - when finished! - #. **STEPS TO RUN SUCCESSFULLY** *(also written on script!)* + * 2A) Command 1: change edf_filename variable + ``edf_filename = ‘C:\Users\ncl24\Box\CoganLab\D_Data\GlobalLocal\D103\240110 COGAN_GLOBALLOCAL.EDF’;`` - * **Step 1** : **Copy EDF file into D_Data Box folder!** (from TaskUploadDir) + * 2B) Command 2: change h variable + ``h = edfread_fast(‘C:\Users\ncl24\Box\CoganLab\D_Data\GlobalLocal\D103\240110 COGAN_GLOBALLOCAL.EDF’);`` - * **KEY** - Make sure EDF file is copied into the **D_Data** Subject Global Local folder on Box! - * **Step 2**: **Edit info** (specific to each subject) + **copy in command line to run each command below (A, B, C) ONE AT A TIME:** + * 2C) Command 3: run makeTrials_GL function + ``makeTrials_GL(‘D103’, ‘240110’)`` - * 2A) Command 1: change edf_filename variable - ``edf_filename = ‘C:\Users\ncl24\Box\CoganLab\D_Data\GlobalLocal\D103\240110 COGAN_GLOBALLOCAL.EDF’;`` + #. Must replace: (‘subject’, ‘taskdate’) 1. Replace **subject** with + **‘D#’** 2. Replace **date** with **‘taskdate’** + (e.g. **‘230807’)** + #. Final format: **makeTrials_GL(‘D#’, ‘taskdate’)** 1. **Example** : + D94 - * 2B) Command 2: change h variable - ``h = edfread_fast(‘C:\Users\ncl24\Box\CoganLab\D_Data\GlobalLocal\D103\240110 COGAN_GLOBALLOCAL.EDF’);`` + #. subject = ‘D94’ + #. date = ‘230807’ + #. **=** :**makeTrials_GL(‘D94’, ‘230807’)** - * 2C) Command 3: run makeTrials_GL function - ``makeTrials_GL(‘D103’, ‘240110’)`` + #. You **MUST add the single ‘quotations’** around each of the real + variables that you enter, in order for them to be registered as + the values for those variables! 4. *Once 2C is finished running, + you are done!* - #. Must replace: (‘subject’, ‘taskdate’) 1. Replace **subject** with - **‘D#’** 2. Replace **date** with **‘taskdate’** - (e.g. **‘230807’)** - #. Final format: **makeTrials_GL(‘D#’, ‘taskdate’)** 1. **Example** : - D94 + * **Final output** = **Trials.mat** (when 2C is done ^) - #. subject = ‘D94’ - #. date = ‘230807’ - #. **=** :**makeTrials_GL(‘D94’, ‘230807’)** + #. **Trials.mat** file will automatically save under the **taskdate (e.g. 230807) → matfolder on**\ \*\* Box \****!*\* + #. Example path to locate Trials.mat file: - #. You **MUST add the single ‘quotations’** around each of the real - variables that you enter, in order for them to be registered as - the values for those variables! 4. *Once 2C is finished running, - you are done!* + * Box -> CoganLab -> D_Data -> GlobalLocal -> D103 (subj) -> 240110 + (taskdate) -> mat -> Trials.mat - * **Final output** = **Trials.mat** (when 2C is done ^) + * If you would like to save it in your local PC folder (InUnit + Preprocessing) as well, you can download the file from Box and copy + it there! – you don’t have to though. - #. **Trials.mat** file will automatically save under the **taskdate (e.g. 230807) → matfolder on**\ \*\* Box \****!*\* - #. Example path to locate Trials.mat file: +Step 6: BIDS_coding (WSL → Visual Studio (VS) Code program) +---------------------------------------------------------- +*BIDS* - * Box -> CoganLab -> D_Data -> GlobalLocal -> D103 (subj) -> 240110 - (taskdate) -> mat -> Trials.mat +#. Open WSL - * If you would like to save it in your local PC folder (InUnit - Preprocessing) as well, you can download the file from Box and copy - it there! – you don’t have to though. +#. Open ``BIDS_coding`` workspace (folder from Desktop) -* **Step 6: BIDS_coding (WSL → Visual Studio (VS) Code program)** - *BIDS* + * **File** (top left) → **Open Folder → Desktop → BIDS_coding** - #. Open WSL + #. Make sure it opens into **BIDS_convert_wsl.sh** script! - #. Open ``BIDS_coding`` workspace (folder from Desktop) + #. **BIDS_coding → BIDS_converter → BIDS_convert_wsl.sh** - * **File** (top left) → **Open Folder → Desktop → BIDS_coding** + #. C:/Users/ncl24/BIDS_coding/BIDS_converter/BIDS_convert_wsl.sh - #. Make sure it opens into **BIDS_convert_wsl.sh** script! +#. In "**Terminal**" (command window at bottom), type ``git pull`` - #. **BIDS_coding → BIDS_converter → BIDS_convert_wsl.sh** + * Make sure you are in the right workspace, should look like this: - #. C:/Users/ncl24/BIDS_coding/BIDS_converter/BIDS_convert_wsl.sh + #. |image4| + #. Press **Enter** - #. In "**Terminal**" (command window at bottom), type ``git pull`` +#. If you encounter an **error message!** - * Make sure you are in the right workspace, should look like this: + #. *Message*: + |image8| - #. |image4| - #. Press **Enter** + #. You will need to make sure all of your changes to **ALL scripts in the workspace** + (modified files will have an "**M**" next to them + in explorer left side bar) have been **COMMITTED** to Github + **before running** the next line, because they will be + **ERASED!!!** + * *To commit changes to github*: type ``git push`` → ``git commit`` - #. If you encounter an **error message!** + #. If your only changes are the variables of subject, task, etc. that + you make for specific subjects, then you don’t have to commit them – + **BUT** , make sure any files you have run for previous subjects + with the script are **SAVED TO BOX BEFORE RUNNING the next command** + , because they will be **overwritten!!!** 1. To Save to Box: - #. *Message*: - |image8| + * Drag **sub-D00XX** folder into **share** folder above Workspace + in WSL explorer → should be in **Share** folder on Desktop, then + copy into Box → **BIDS-1.1_GlobalLocal** folder - #. You will need to make sure all of your changes to **ALL scripts in the workspace** - (modified files will have an "**M**" next to them - in explorer left side bar) have been **COMMITTED** to Github - **before running** the next line, because they will be - **ERASED!!!** - * *To commit changes to github*: type ``git push`` → ``git commit`` +#. Once all previous subject files have been saved to Box BIDS + Global Local folder, you will reset the script! - #. If your only changes are the variables of subject, task, etc. that - you make for specific subjects, then you don’t have to commit them – - **BUT** , make sure any files you have run for previous subjects - with the script are **SAVED TO BOX BEFORE RUNNING the next command** - , because they will be **overwritten!!!** 1. To Save to Box: + #. Type ``git reset --hard`` + Enter! + #. *Should look like this when idone*: + |image2| - * Drag **sub-D00XX** folder into **share** folder above Workspace - in WSL explorer → should be in **Share** folder on Desktop, then - copy into Box → **BIDS-1.1_GlobalLocal** folder +#. When git reset is done, **re-type git pull** + Enter! - #. Once all previous subject files have been saved to Box BIDS - Global Local folder, you will reset the script! +#. **KEY** – **Edits to make to Script after Reset** : - #. Type ``git reset --hard`` + Enter! - #. *Should look like this when idone*: - |image2| + #. Editing **BIDS_convert_wsl.sh** script! - #. When git reset is done, **re-type git pull** + Enter! + #. **EDITS** : *CRITICAL TO CHANGE THESE IN SCRIPT BEFORE RUNNING!* + #. **Line 4** : Change task to → **TASKS=(“GlobalLocal”)** + #. Must change from “SentenceRep” default to GlobalLocal (or any + task going forward) + * Use the exact same name as the D_Data folder! + #. **Final** : |image1| - #. **KEY** – **Edits to make to Script after Reset** : + #. **Line 16** : **Comment out (#) whole** **mapfile** **line!** - #. Editing **BIDS_convert_wsl.sh** script! + #. Don’t need for Global Local (will cause error) + #. **Final** : *see full line on script* |image0| - #. **EDITS** : *CRITICAL TO CHANGE THESE IN SCRIPT BEFORE RUNNING!* - #. **Line 4** : Change task to → **TASKS=(“GlobalLocal”)** - #. Must change from “SentenceRep” default to GlobalLocal (or any - task going forward) - * Use the exact same name as the D_Data folder! - #. **Final** : |image1| + #. **Line 17** : Change **SUB_IDS=(D#)** D# to correct Subject D#’s! - #. **Line 16** : **Comment out (#) whole** **mapfile** **line!** + #. Can run **multiple subjects at once** , or just **one** + #. If running multiple, separate by spaces only! No comma! → *see + example below:* + #. **Final** : |image5| - #. Don’t need for Global Local (will cause error) - #. **Final** : *see full line on script* |image0| + #. **Line 35** : **Comment out (#) the whole line 35!** - #. **Line 17** : Change **SUB_IDS=(D#)** D# to correct Subject D#’s! + #. Global Local doesn’t have task stimuli, so don’t need this line + and it will cause an error if you keep it! + #. **Final** : *see full line on script* |image6| + #. Only comment this out for Global Local or tasks that don’t have + task stimuli! + * For other future tasks that do, change the ``“sentence_rep”`` task + name in the middle of the command line (35) and insert the + correct task name to use proper task stimuli! - #. Can run **multiple subjects at once** , or just **one** - #. If running multiple, separate by spaces only! No comma! → *see - example below:* - #. **Final** : |image5| + #. **CTRL + S** TO SAVE ALL EDITS TO SCRIPT!!! - #. **Line 35** : **Comment out (#) the whole line 35!** +#. When all edits have been made to script & saved ( **ctrl + s** ), type ``conda activate BIDS_coding`` + Enter! - #. Global Local doesn’t have task stimuli, so don’t need this line - and it will cause an error if you keep it! - #. **Final** : *see full line on script* |image6| - #. Only comment this out for Global Local or tasks that don’t have - task stimuli! - * For other future tasks that do, change the ``“sentence_rep”`` task - name in the middle of the command line (35) and insert the - correct task name to use proper task stimuli! +#. The conda activate command will change (base) at the start + of the command path to (BIDS_coding) - #. **CTRL + S** TO SAVE ALL EDITS TO SCRIPT!!! + * Once the new command line pops up below: + * Type ``cd BIDS_converter`` + Enter! - #. When all edits have been made to script & saved ( **ctrl + s** ), type ``conda activate BIDS_coding`` + Enter! +#. within BIDS_coding (adds it to end of path), which is where you can + now run the script to perform the BIDS conversion functions - #. The conda activate command will change (base) at the start - of the command path to (BIDS_coding) + * Once the next command line pops up below with /BIDS_converter at the + end: type ``./BIDS_convert_wsl.sh`` + Enter! - * Once the new command line pops up below: - * Type ``cd BIDS_converter`` + Enter! +**STEPS 8, 9, 10 SHOULD LOOK LIKE THIS** : (in order top → bottom!) - #. within BIDS_coding (adds it to end of path), which is where you can - now run the script to perform the BIDS conversion functions + |image7| - * Once the next command line pops up below with /BIDS_converter at the - end: type ``./BIDS_convert_wsl.sh`` + Enter! +#. The script should then run for a few minutes (10-15 min) + after entering the last command to create all of the converted BIDS + files! - **STEPS 8, 9, 10 SHOULD LOOK LIKE THIS** : (in order top → bottom!) + #. Final output will be on the left side bar (WSL Explorer) 1. *To open + explorer*: click double paper icon at top left corner - |image7| + #. Under **ncl24 → Workspace → GlobalLocal → BIDS** 1. Locate the + **sub-D0XXX** folder! - #. The script should then run for a few minutes (10-15 min) - after entering the last command to create all of the converted BIDS - files! + #. i.e. sub-D0100 for Subject D100 + #. |image9| - #. Final output will be on the left side bar (WSL Explorer) 1. *To open - explorer*: click double paper icon at top left corner + * This is where all of the finalized BIDS files will go! - #. Under **ncl24 → Workspace → GlobalLocal → BIDS** 1. Locate the - **sub-D0XXX** folder! +#. Last step: move to **share** folder (on WSL) - #. i.e. sub-D0100 for Subject D100 - #. |image9| + * When it is finished creating BIDS files, in the left side bar with + workspaces, drag and drop this **sub-D00XX** output folder + containing the BIDS files into the " **share**" folder above + Workspace! (see top of pic above) 1. Then you will be able to access + it from **Share PC** folder on Desktop! → if not moved to share, + can’t access on Windows - * This is where all of the finalized BIDS files will go! - - #. Last step: move to **share** folder (on WSL) - - * When it is finished creating BIDS files, in the left side bar with - workspaces, drag and drop this **sub-D00XX** output folder - containing the BIDS files into the " **share**" folder above - Workspace! (see top of pic above) 1. Then you will be able to access - it from **Share PC** folder on Desktop! → if not moved to share, - can’t access on Windows - -* **Final Step: Upload sub-D00XX on Share folder to Box BIDS-1.1_GlobalLocal** +Final Step: Upload sub-D00XX on Share folder to Box BIDS-1.1_GlobalLocal +------------------------------------------------------------------------- * Copy **sub-D00XX** with all finalized BIDS file outputs from **Share** PCfolder into **Box → CoganLab → BIDS-1.1_GlobalLocal →