I have written a tcl script, ResultViewer.hx
, based on work from Steffen Prohaska that allows
There is also a related simpler script StackViewer which simply allows rapid scanning through a directory of confocal scripts.
git clone git@bitbucket.org:jefferis/resultviewer.git
somewhere sensible/Volumes/JData/JPeople/Steffen/2011-07-29_InitBrainPosGHT
TemplateStem.surf
in the hx subfolderimages4um
that is next to the folder containing registrations e.g.${refbrain}_${brainkey}_${chan}_${regtype}.list
IS2_AABD4-1_01_9dof.list
the key would be AABD4-1
src/ResultViewer.hx
onto Amira to get started/Volumes/JData/JPeople/Steffen/2011-07-29_InitBrainPosGHT/src/ResultViewer.hx
if you are using the JData version./Volumes/JData/JPeople/Aaron/YourRegistrationFolder/Registrations/IS2/Registration
/Volumes/JData/JPeople/Aaron/YourRegistrationFolder/Registrations/IS2/Registration/mynicebrains.txt
.list
(${refbrain}_${brainkey}_${chan}_${regtype}.list
)munger.pl
's -H
switchimages4um
(though you can choose any voxel size you want within reason)NrrdResample(<infile>,<outdir>,voxdims=c(2,2,2))
mynicebrains.txt
this will make a file called mynicebrains.txt-sel.txt
mynicebrains.txt-sel.txt
it will make a backup called mynicebrains.txt-sel.txt.bak
mynicebrains.txt-sel.txt.bak
it will be overwrittenIf the existing registration is poor (or non-existent) you can often make a good one using Amira's surface based registration
curbrainview
(volume rendering) so you can see more clearlycurbrain.surf
curbrain.AlignSurfaces
rigid
rigid + unifiorm scale
affine
curbrain.AlignSurfaces
affine