====== 7T MRSI PFC Files  ======

[[:tools:pfc|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:
<code>
/Volumes/Hera/Projects/7TBrainMech/subjs/10129_20180917/slice_PFC/MRSI_roi/13MP20200207/MP
</code>

===== 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 [[:tools:lcmodel]] and then included in [[:grants:7t:data]]. 


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''


<code>
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
</code>

===== 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'' | |