Hello everyone,

I am currently trying to register our lab's 2 photon imaging data of zebrafish larve onto a template.
My template is iteratively averaged by 10 z brain stacks on cmtk.
The objective is to register our experiment's calcium imaging activity time series(should be 1-6 planes) onto the template, so my current pipeline consists 3 steps: 
1. register calcium imaging activity experiment recording(1-6 planes, now i only tried 1 plane) onto same fish's z stack.(z stack is acquired right after the experiment recording)
2. register this fish's z stack onto template
3. apply two transformations file on experiment recording and get registered recording

Now the 2nd step I got good result but 1st and 3rd step failed.

Take one registration as example to elaborate, my z stack(zstack_fish1.nii) and template(template.nii) file size are both 1024x1024x101, there are 101 z planes from top to bottom of fish. My experiment recording file(movie_fish1.nii, format converted by figi) size is 1024x1024x924, 924 means it have 924 timepoints. It is a recording of one z plane roughly located between 39th-41th z plane of zstack_fish1.nii file. These files are attached(movie is too big, only attach one frame of movie).
Now zstack_fish1.nii(1024x1024x101) to template.nii(1024x1024x101) registration run successfully. But for movie_fish1.nii(1024x1024x924) to zstack_fish1.nii registration, i have tried following and get bad results:

1. rigid registration directly, result is a whole black file(1024x1024x101)
/usr/lib/cmtk/bin/registration --echo --initxlate --auto-multi-levels 5 -v --dofs 6 --dofs 9 -o affine1.xform zstack_fish1.nii movie_fish1.nii
WARNING: dimension 4 is greater than 3 in file movie_fish1.nii
Entering resolution level 1 out of 6...
Entering resolution level 1 out of 6...
Entering resolution level 2 out of 6...
Entering resolution level 2 out of 6...
Entering resolution level 3 out of 6...
Entering resolution level 3 out of 6...
Entering resolution level 4 out of 6...
Entering resolution level 4 out of 6...
Entering resolution level 5 out of 6...
Entering resolution level 5 out of 6...
Entering resolution level 6 out of 6...
Entering resolution level 6 out of 6...
Resulting transformation parameters:
#0d: 0.000000
#1d: 3.148835
#2d: 148.409010
#3d: 0.000000
#4d: -0.067115
#5d: -0.122770
#6d: 1.000000
#7d: 1.000049
#8d: 1.000000
#9d: 0.000000
#10d: 0.000000
#11d: 0.000000
#12d: 169.539899
#13d: 169.539899
#14d: 0.000000

/usr/lib/cmtk/bin/reformatx --echo --sinc-cosine -o result1.nii --floating movie_fish1.nii zstack_fish1.nii affine1.xform
WARNING: dimension 4 is greater than 3 in file movie_fish1.nii

result1.nii is a whole black file(1024x1024x101)

2.pick one frame of movie(f1_trace_100.nii, generated by figi, 1024x1024) to register, result is still whole black as result1.nii
/usr/lib/cmtk/bin/registration --echo --initxlate --auto-multi-levels 5 -v --dofs 6 --dofs 9 -o affine2.xform zstack_fish1.nii f1_trace_100.nii
Entering resolution level 1 out of 6...
Entering resolution level 1 out of 6...
Entering resolution level 2 out of 6...
Entering resolution level 2 out of 6...
Entering resolution level 3 out of 6...
Entering resolution level 3 out of 6...
Entering resolution level 4 out of 6...
Entering resolution level 4 out of 6...
Entering resolution level 5 out of 6...
Entering resolution level 5 out of 6...
Entering resolution level 6 out of 6...
Entering resolution level 6 out of 6...
Resulting transformation parameters:
#0d: 0.000000
#1d: 3.148835
#2d: 148.541592
#3d: 0.012584
#4d: 0.033557
#5d: 0.114850
#6d: 1.000000
#7d: 1.000000
#8d: 1.000000
#9d: 0.000000
#10d: 0.000000
#11d: 0.000000
#12d: 169.539899
#13d: 169.539899
#14d: 0.000000

/usr/lib/cmtk/bin/reformatx --echo --sinc-cosine -o result2.nii --floating f1_trace_100.nii zstack_fish1.nii affine2.xform

the result file is the same as result1.nii, whole black 1024x1024x101

3. pick one frame of movie, and register to one plane of zstack(40/101), generate a single black plane
After this, i saw forum and noticed Prof. Jefferis mentioned CMTK only deal with 3d volume, so i will not put details here.

I hope after 3 steps, my final results could be registered 1024x1024x924 file, still one plane and 924 timepoints, or 1024x1024x101x924 file, contain all zstacks(only warped recording plane have signal, other are blank planes) and 924 timepoints, I would like to know whether it could be implemented in cmtk or cmtk gui.

I would really appreciate it if you could help with it! Thanks a lot!

Best,
Yuxin