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1. From the SPM 12 menu, Select CSPM from the Toolbox drop down list. Select Projects under the Complete database functions
   
   
   
2. Select the Project name: OSA2013 and click Configure
   1. This will group all the Subjects in the OSA2013 study
   
   
   
3. A Project Configuration Window will appear
   
   1. Step 1: Identify the Group Condition: Control, OSA, Control_REP or OSA_REP
      1. NOTE: At this time you we will not pair any of the scans in the REP group
   2. Step 2: Select the Subject
      1.  For this example, we selected OSA3160
   3. Step 3: Select the appropriate scans corresponding to the Subject's specific study visit under the Available MRIs List
      1. Subjects who have completed multiple MRI scans will have all of their scans included in this list
         1. Note the scans completed in 2014 and 2015 for this Subject
      2. Highlight the second T1 scan (Series 6). Remember some subjects may have more than T1 series recorded. By selecting this series you are saying that the second T1 is the scan we want to analyze
   4. Step 4: Identify the MRI scan with the correct MRI Type name
      1. Since the name of the scan is a T1 we select  T1 from the MRI Type options. This will identify the T1 as a T1 scan.
      2. Although the BMC uses DWI to label DTI scans, we identify these scans as DTI.
   5. Step 5: Click Add
   6. Step 6: Notice the the T1 scan you selected in Step 3 is now available in the MRI's in Study box
4. Repeat Steps 4-6 for the remainder of the MRI scans completed by that subject according to that specific MRI visit.
   
   
   
5.  The MRI's added to theStudy box should list all of the scans completed for that specific study visit.
   1. Scans highlighted in orange imply that an additional step is required to complete the scan in Matlab
      
      
6. For fMRI scans completed on or after 2017 at BMC, follow these steps:
   1. 1. Step 1: Identify the Group Condition: Control, OSA, Control_REP, OSA_REP, OSA IMT PRE, OSA IMT POST
         1. NOTE: At this time you we will not pair any of the scans in the REP group
      2. Step 2: Select the Subject
         1.  For this example we selected OSA3227
      3. Step 3: Select the appropriate scans corresponding to the Subject's specific study visit under the Available MRIs List
         1. Subjects who have completed multiple MRI scans will have all of their scans included in this list
            1. Note the scans completed in 2014-2017 for this Subject 
         2. Highlight the T1 series with no motion, artifact present
            1. NOTE: It is preferred to record the scan without any motion, artifact
            2. NOTE: If "motion, artifact" is present on all T1 scans, add all the T1 scans available from that session
            3. NOTE: Refer to the comments below the Available MRIs List to verify if motion, artifact was present during Subject's T1 scan
      4. Step 4: Identify the MRI scan with the correct MRI Type name
         1. Since the name of the scan is a T1 we select T1 from the MRI Type options. This will identify the T1 as a T1 scan.
         2. Although the BMC uses DWI to label DTI scans, we identify these scans as DTI.
         3. Select ASL for scans labeled as ASL REST
         4. Select fMRI for the fMRI rest and functional scans (Handgrip ,Valsalva BreathHold, Insp Loading, & Stroop).
         5. ASL, fMRI REST, and all functional scans will appear highlighted in orange   
            1. Scans highlighted in orange indicate that we need to additional information about that scan. In other words we need to state what happened during that scan. 
            2. For fMRI REST scans: 
               1. Select the highlighted scan
               2. Click on the inverted triangle below the MRI's in Study box to access the fMRI Edit Types dropdown list
               3. Scroll down and select the HCP 2017- Resting Total scans option from the dropdown menu  
                  
               4. Notice that the scan is now highlighted in grey and indicates a specific TYPE of fMRI scan in the fMRI Edit Type field. You have now specified that this scan corresponds to the resting state.
            3.  For ALL FUNCTIONAL scans: 
               1. Select the highlighted scan
               2. Click on the inverted triangle below the MRI's in Study box to access the fMRI Edit Types dropdown list  
               3. Scroll down and select the HCP 2017- Hand grip total scans option from the dropdown menu  
               4. 
               5. Notice that the scan is now highlighted in grey and indicates a specific TYPE of fMRI scan in the fMRI Edit Type field. You have now specified that this scan corresponds to the handgrip.
               6. 
               7.  Repeat for remaining functional scans
            4.  NOTE: At this time do not pair ASL with sequence from the drop-down menu

         6. NOTE: At this time we will not pair any of the following scans: HCP Spin Echo Field Map, T2w SPC, TSE HiResHp, Field Mapping GRE, & Field Mapping GRE phase

      5. Step 5: Click Add (Keyboard Shortcut→ Letter "A")
      6. Step 6: Notice the the T1 scan you selected in Step 3 is now available in the MRI's in Study box
   2. Repeat Steps 4-6 for the remainder of the MRI scans completed by that subject according to that specific MRI visit.
      

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1. If a Subject needs to be added to the Subject Group:
   
   1. Type the Subject Name and press Enter from the Add new study box on the left hand side of the menu
   2. Pressing Enter will search the database for the Subject with that specific condition and 4 digit number. If the Subject has been entered in the Subjects and Data window their name will appear from the Subject drop down menu.
   3. Click Add
      
      
      
      
2. Matlab will take a few seconds to add the new Subject into the OSA Study group. The new subject will appear in the list of subjects by group.
   
   
   
   
3. You have successfully added a new subject to the group. Proceed with Steps 3-5 above.
4. To delete a scan from the MRI's in Study list, highlight the scan, and select delete. Matlab will prompt you to a confirmation window asking if you would like to delete scan. Select delete.

If Matlab indicates that no anatomical T1 scans are present

1. Highlight the T1 scan on the Subject & Info window
   
   1. Select View 
      1. This option opens two windows showing you that there is a file in that folder. Note that the raw folder has the dicom files 
2. This typically occurs when 2-T1 scans are present in the Subject & Info window or when there is movement present in the scan 
   1. If 2 -T1 scans are present: 
      1. Delete the 4th scan and keep the 2nd. Doing so also deletes the 4th scan from the Projects window
      2. Note: Sometimes 2-4 T1 series are generated per scan during each MRI scanning session. If one T1 was collected, each scan has 4 series, and we document the 2nd series on Matlab 
   2. If there is movement present: 
      1. Our MRI team will repeat the T1 scan due to artifact 
         1. In this scenario, we take the average of all the remaining T1 scans
3.  Label T1 scan as a T1 on the Subject & Info window and label the scan we are analyzing 

Copy & Convert Project

To Create & Send Patient Images

1. From CSPM menu, Select Copy and Convert  from the view MRI & Subject Info box
   1. This will take all the data from the raw data folder to the projects folder
2. From CSPM menu, Select Patient Images from the view MRI & Subject Info box
   
   
   
3. Complete the following steps in the CSPM Brain Pictures Menu
   
   1. Step 1: Save the MRI images to the D Drive under the Working/Patient Images CSPM folder
      
   2. Voxel Size: Enter 111
   3. Movie Details: Enter the following:
      
      1. FPS: 30
      2. Rotation Step (degrees): 1
      3. Time for slices (sec): 10
      4. T1 threshold: 5
4. Select Run
5. The program will run load project information from the database and create patient images for all the Subjects with MRI scans. This process may take a few hours to complete.
   
   
   
6. The patient images will now appear in the D Drive as shown below:
   
   
   
7. Copy & Paste the two files in the "Add files to subject" folder to each patient image folder in the D Drive
   
   
   
8. Create a zip folder for each individual patient image folder
   
   1. Highlight all folders using the Ctrl/Shift key
   2. Right click using your mouse and select 7-Zip & Add to "......".zip
       
      
      
9. Windows will compress all the folders into 1 individual folder 
   
   
   
10. Open a new browser and login into the OSABrainStudy BOL UCLA account. Access the BMC MRI Image folder in the Google Drive.
11. Upload all the zip folders from the D Drive to the google drive. 
    
    
    
12. Create a shared link by modifying shared settings for each individual zip folder.
    
    1. Select the Subject Zip folder and select Share
    2. Google will prompt you to a shared screen, Select Advanced from the bottom right
       
    3. From the Shared Settings, Select Change 
       
       
       
    4. From the Link sharing window select  Anyone with the link can access.
       
       1. Under Access: Select Can Edit
          1. This option will allow Subjects to download the folder from the link
       2. Save
       
       
       
13.  Compose an email on Thunderbird. Label the Subject field: UCLA MRI STUDY: MRI IMAGES
    
    1. Attach the Downloading Zipfolder from Google Drive jpeg image from the PD desktop or Google Drive → Data Collection: MRI
    2. Copy & Paste the MRI images email the OSAbrainresearch google drive to the body of the message
    3.  Return to the uploaded zip folder on OSAbrainstudy google drive
       
       1. Right click and select Share & Share with others
          
       2. Click on Copy Link
          
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15. Enter the Subjects name & email address. Send email.
    
    

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