Converting a Single Coordinate from Paxinos to DSURQE to Allen - CoBrALab/documentation GitHub Wiki

All code for these steps can be found in /data/chamal/projects/natvik/sir_voxel/analysis/paxinos_to_DSURQE_to_allen \ Input: single Paxinos coordinate.
Example:
Dorsal striatum stereotaxic coords:
+0.2 mm relative to bregma (y)
+2.0 mm from the midline (right hemisphere) (x)
-2.6 mm from the brain surface (depth) (z) \

Input / Creating a .mnc Tag File from a Single Coordinate

  1. Create a .tag file using minctools register
    -- module load minc-toolkit-v2
    -- register /data/chamal/projects/elisa/DSURQE_to_Paxinos_mouse/DSURQE_like_paxinos.mnc
    -- enter paxinos coordinates above (x/y/z) into the dialog box above
    image
    -- save output as a .tag file (output.tag in this example) in the box above "Save Tags"
    -- add "1 1 1" at the end of the one line of text in the .tag file to enable conversion into a .mnc voxel file
    -- cat output.tag should yield an output something like this:
    MNI Tag Point File Volumes = 1; Points = 2 -2.5 -1.8 1 1 1;
    -- load template + tag using Display and convert into .mnc
    -- Display /data/chamal/projects/elisa/DSURQE_to_Paxinos_mouse/DSURQE_like_paxinos.mnc
    -- File --> Load Labels .tag (select output.tag from above) --> Save Labels .mnc (create a new .mnc file, ex: output.mnc)

Algorithm

-- May need to dilate .mnc tag file from above 2-3 times for it to work with ANTs
-- mincmorph -dilation output.mnc output_dilated.mnc
-- mincmorph -dilation output_dilated.mnc output_dilated2.mnc \ -- etc.
-- run ./resample.sh -- separate transforms to go from Paxinos --> DSURQE (based on Elisa's old work) and DSURQE to Allen (python script transform_space_gabe.py based on a combination of Gabe and Yohan's more recent work) -- run Gabe's code, use mincmorph

Output

-- should be a single binary voxel
-- confirm by registering with Allen template
-- may need to dilate before resampling to a different resolution / before finding an overlapping allen tracer image