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  • Using MNI Register to Manually Register Volumes
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MNI-register is an interactive program to display and merge 2 volumes and pick homologous points for manually registering one volume to the other (https://github.com/BIC-MNI/Register).

Historically, the TissueVision machine sometimes restarted in the middle of acquiring slices of a brain. As such, only the slices within each period of continuous acquisition are aligned. Although TV_pipeline.py provides a default method for aligning the two sections, it can be inadequate so we can use MNI-register to manually register the two slices before and after the machine's restart. For example:

$ register /hpf/largeprojects/MICe/nwang/TV_HPF/output/sections_cellprofiler/F_07/F_07_Z0164_smooth.mnc /hpf/largeprojects/MICe/nwang/TV_HPF/output/sections_cellprofiler/F_07/F_07_Z0165_smooth.mnc

The GUI below will pop up; the first volume is on the left, the second volume is in the middle, and they are superimposed on the right. Left click corresponding points on the two volumes and right click to tag them. Tag many points to reduce the average error and make sure to use the whole brain, but avoid tagging ambiguous structures. You may save the transform directly, but I prefer to save the tags to a text file first. On the top left, type the name of the tag file "L164_R165" to save the tags as "L164_R165.tag" in the current working directory.

To obtain an lsq6 transform, use the command:

$ tagtoxfm -lsq6 L164_R165.tag L164_R165.xfm

Lastly, resample the slices:

$ mincresample -transform L164_R165.xfm -like /hpf/largeprojects/MICe/nwang/TV_HPF/output/sections_cellprofiler/F_07/F_07_Z0164_smooth.mnc /hpf/largeprojects/MICe/nwang/TV_HPF/output/sections_cellprofiler/F_07/F_07_Z0165_smooth.mnc /hpf/largeprojects/MICe/nwang/TV_HPF/output/sections_cellprofiler/F_07/F_07_Z0165_smooth_transformed.mnc

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