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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, OSA POST IMT
         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 (change image to show motion, artifact in comments)Image Added
      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. 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.
      Image Added

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.

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To Convert Images (REVISE)

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