====== PFC ROI Placement ======
ROI placement on top of PFC scout preformed manually. PFC slice orientation at acquisition is positioned by [[:tools:qpasaslicewarp]]. For files organization see [[:tools:pfc:files]].

===== How to place coordinates =====

You will have 2 windows open simultaneously: coordinate placing GUI and spectrum visualization GUI

==== Opening the coordinate placement GUI ====

  * Connect to [[:admin:it:rhea]] in the terminal (see [[admin:remoteaccess]])
  * Navigate to the MRSI_roi directory (''cd /Volumes/Hera/Projects/7TBrainMech/scripts/mri/MRSI_roi'')
  * Run the coord_builder program (the coordinate placement GUI) (e.g., ''./coord_builder.bash view 10129_20180917 ROI_mni_13MP20200207.nii.gz'')


==== Opening the spectrum GUI ====

  - Open new terminal window and connect to rhea again
  - Open ''matlab'' (just type matlab in the terminal)
  - Once matlab is open type: ''cd /opt/ni_tools/matlab_toolboxes/sid3_MRRC/'' then ''def4'' then ''hgload new10''

==== Once the spectrum GUI is open ====

  * File name SI = SI array file for that subject (e.g., /Volumes/Hera/Projects/7TBrainMech/subjs/[subject]/slice_PFC/MRSI_roi/raw/siarray.1.1)
  * File name scout and File name image (same file): /Volumes/Hera/Projects/7TBrainMech/subjs/[subject]/slice_PFC/MRSI_roi/raw/seg.7
  * Change resolution to 216 in “Scout Res” box and the “Image” box next to it
  * Click first 3 load buttons
  * Click first integrate button
  * Click on the bottom left brain to pop the grid up and get placing!
  * Use the < and > arrows to make the spectrum look normal
  * Use X2 and /2 buttons to zoom in and out to make spectrum bigger and smaller so you can examine it


====  AFNI check  ====

  * When you think you're done placing, click 'mni' and it will pop open AFNI so you can use the 'whereamI' feature to check your roi placement 
  * cross-ref the T-T atlas 
  * If all good, you can close afni and you're done with the AFNI check portion.
  * If not all good, you can still close afni but go back to coordinate placer and move your coordinates to the correct spots.
  * Click mni to check again and start this process over again. Repeat until satisfied with ROI locations.


==== Saving out spectrum files  ====

  * click 'save'!
  * click 'spectrum'! 
  * If you don't do these things, all your hard work will be for naught! PLZ click save and spectrum.

=== Visual things to look for ===

  * Cho and Cre peaks to the left and NAA peak to the right, but no lipid peak
  * fuzzy/split peaks which indicates motion
  * NOTE: all STS data will be garbage; that’s fine, just ignore it, we don’t use it. Shimming was not optimized for back of the brain at time of acquisition, so you do NOT need to place STS coordinates or really care about them. 
  * Examples: https://docs.google.com/presentation/d/1ZNZvT-EYEWkQGC2SoRZBcnTB3WBpQ-WLrS3yqLEFL0s/edit#slide=id.p


=== Other stuff/ Good resources  ===

  * [[https://docs.google.com/spreadsheets/d/1UlOZxnR4NJzJ5rcvbsaRl2JHqBr9gKQDy7RUj-2KKTo/edit#gid=0|Coordinates placements sheet]]
  * code
    * [[https://github.com/LabNeuroCogDevel/MRSIcoord.py]] and on [[https://github.com/LabNeuroCogDevel/allscripts/tree/master/root/Volumes/Hera/Projects/7TBrainMech/scripts/mri/MRSI_roi|all_scripts]]
    *  ''rhea:/Volumes/Hera/Projects/7TBrainMech/scripts/mri/MRSI_roi''
    * check out journal club presentation from 2020 on MRS in general. Some stuff is outdated re: our finalized pipeline but MRS 101 stuff still applies. https://lncd.pitt.edu/wiki/doku.php?id=journal_club_presentations

==== Cite  ====

** If you use/need to describe these methods, you can cite Perica et al (2022). I would, you know, like appreciate it or whatever. **
https://www.sciencedirect.com/science/article/pii/S0301008222001563

From the methods of that paper: 

> "Regions of interest (ROIs) were defined in MNI-space using a custom ROI atlas, and included right and left dorsolateral prefrontal cortex (DLPFC), right and left anterior insula (AI), anterior cingulate cortex (ACC), and medial PFC (MPFC) (Fig. 1b). An automated nonlinear registration using FSL’s FNIRT was performed to map those ROIs into each subject’s native space. ROI centers were visually inspected and manually adjusted for each subject with in-house developed software in order to maximize spectral quality and gray matter content of the voxel. To ensure manual adjustment did not move ROI centers outside of the region of interest, the adjusted ROIs were registered back to standard space where their position was confirmed with the Eickhoff-Zielles maximum probability map of the Talairach-Tournoux atlas using AFNI’s whereami (Cox, 1996). The ROI coordinates were then used in the anatomically guided voxel-shifting reconstruction of MRSI data (Hetherington et al., 2007) to gather spectroscopic data over the ROI."

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===== Backlinks =====

{{backlinks>.}}