…nts in place but is still waiting for WarpMapper and its final form.

… nearest-neighbor

…ented anatomicals are saved in the anat_dir, not /tmp, and the commands are printed for debugging use. in future the anatomicals may be saved to /tmp again, since the reoriented versions are not necessary for getting the correct coordinates in the identity transform

…l do, reverted the addition in __init__ also

…commit). reorients anatomicals, does flirt, feeds this to fnirt, saves the resulting warpfield in the database. then samples the warp field to get a Volume of translations, maps this to vertices, and creates arrays corresponding to the pts array but with the MNI coordinates, not the anatomical ones. saves this as a surfinfo in the database.

…e of the mesh

… a picked vertex.

…o removed extraneous argument.

…an brings up the MNI coords box for the selected vertex. Coordinates are editable, and hitting enter or Submit looks up the nearest MNI coordinate using a kdTree of MNI points which was previously created. It then adds a marker there.

…ands.

…xists.

… are now stored in a per-session tempfile, so they don't permanently clutter the db but are still safe for multiple sessions. some unneeded parameters and imports were removed. additional comments were added, and the do parameter, which allows the function to be run in dummy mode if False.

…rds...

…te box is left out of the template. I verified that the picker still works in this case.

…NI or magnet isocenter coords, hooked this button up to a function that toggles the coordinate display, made the picker smarter also so that it displays the selected coordinates and not MNI every time.

…ways searched for nearest mni coordinate. that has been fixed now, meaning one can search by MNI and magnet iso-center coords.

…return values

…h the picker and the function that reacts to coord space radio button.

…s to mni_nl, wrote some logic to use them, also correctly used the outfile so that get_surfinfo can specify the filename

…rdis-master

…as not being saved in teh appropriate place

… the intermediate file instead. Also fixed the output to match what other surfinfo functions do: now the hemispheres' data are called left and right (instead of leftpts and rightpts), and I transposed them (plus re-transpose in ctm load)

… other set (which i call 'magnet' in the code) is in voxel indices. both of these are correctly displayed and can be searched against and toggled between. also, the selected vertex's coords are displayed in the box after search.

…rdis-master