ROI placement on top of PFC scout preformed manually. PFC slice orientation at acquisition is positioned by MRSI Slice Positioning tool (QPASA). For files organization see 7T MRSI PFC Files.
You will have 2 windows open simultaneously: coordinate placing GUI and spectrum visualization GUI
cd /Volumes/Hera/Projects/7TBrainMech/scripts/mri/MRSI_roi
)./coord_builder.bash view 10129_20180917 ROI_mni_13MP20200207.nii.gz
)matlab
(just type matlab in the terminal)cd /opt/ni_tools/matlab_toolboxes/sid3_MRRC/
then def4
then hgload new10
rhea:/Volumes/Hera/Projects/7TBrainMech/scripts/mri/MRSI_roi
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.”