7T MRSI PFC Files

ROI placement outputs to /Volumes/Hera/Projects/7TBrainMech/subjs/$ld8/slice_PFC/MRSI_roi/$atlas/$initials

where

$ld8 is 5 digit luna id _ 8 digit session date
$atlas is 13MP20200207
$initials are an identify for who placed these coordinage

This looks like:

/Volumes/Hera/Projects/7TBrainMech/subjs/10129_20180917/slice_PFC/MRSI_roi/13MP20200207/MP

Finding the chosen

We may have more than one set of ROI placements. We pick one of them. Those coordinates that are passed on to LC Model and then included in 7T Data: merge_7t.csv.

The final coordinate placement is annotated as a symbolic link /Volumes/Hera/Projects/7TBrainMech/subjs/10129_20180917/slice_PFC/MRSI_roi/LCModel/v2idxfix/13MP20200207_picked_coords.txt

readlink /Volumes/Hera/Projects/7TBrainMech/subjs/1*_2*/slice_PFC/MRSI_roi/LCModel/v2idxfix/13MP20200207_picked_coords.txt |
 sed s/picked_cords.txt$/coords_mprage.nii.gz/g

Files

file	desc
`coords_mprage.nii.gz`	slice pfc cubes affine transformed to match anatomical
`blob-mni.nii.gz`
`cmsphere-mni_labeled.txt`
`cmsphere-mni.nii.gz`
`coords_rearranged.txt`
`coords_slicespace.nii.gz`
`fs_gmmask_mprage.nii.gz`
`fs_gmmask.nii.gz`
`mni_coords_nolabels.txt`
`mni_coords_RAI.txt`
`mni_icbm152_t1_tal_nlin_asym_09c_brain_2mm.nii`
`mprage.nii.gz`
`mprage_warp_linear.nii.gz`
`picked_coords.txt`
`roi_percent_cnt_13MP20200207.txt`
`rorig.nii`
`slice_to_mprage.mat`