I am trying to do image registration and I am using the CMTK Registration GUI plugin developed by the Jefferis Lab (https://github.com/jefferis/fiji-cmtk-gu...).
This plugin creates a command file, but when I try to run the command file, I am getting this error:


ERROR: nrrd library returned error '[nrrd] nrrdLoad: trouble reading "refbrain/refbrain.nrrd"
[nrrd] nrrdRead: trouble
[nrrd] _nrrdRead: trouble reading NRRD file
[nrrd] _nrrdFormatNRRD_read: trouble parsing space directions info |(0.38,0,0) (0,0.38,0)|
[nrrd] _nrrdReadNrrdParse_space_directions: trouble getting space vector 1 of 2
[nrrd] _nrrdSpaceVectorParse: space dimension is 2, but seem to have 3 coefficients
'
ERROR: could not read image geometry from refbrain/refbrain.nrrd
MYEXEC: CMD = /Applications/Fiji.app/bin/cmtk/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/refbrain_DdcGal4_01_9dof.list refbrain/refbrain.nrrd images/DdcGal4_01.nrrd exited with value 1
Aff:DdcGal4_01 INFO: number of threads set to 2 according to environment variable CMTK_NUM_THREADS
ERROR: nrrd library returned error '[nrrd] nrrdLoad: trouble reading "refbrain/refbrain.nrrd"
[nrrd] nrrdRead: trouble
[nrrd] _nrrdRead: trouble reading NRRD file
[nrrd] _nrrdFormatNRRD_read: trouble parsing space directions info |(0.38,0,0) (0,0.38,0)|
[nrrd] _nrrdReadNrrdParse_space_directions: trouble getting space vector 1 of 2
[nrrd] _nrrdSpaceVectorParse: space dimension is 2, but seem to have 3 coefficients
'
ERROR: could not read image geometry from refbrain/refbrain.nrrd
MYEXEC: CMD = /Applications/Fiji.app/bin/cmtk/registration -i -v --dofs 6 --dofs 9 --accuracy 0.4 -o Registration/affine/refbrain_DdcGal4_01_9dof.list refbrain/refbrain.nrrd images/DdcGal4_01.nrrd exited with value 1
Ran 0 initial affine registrations of which 0 failed
Ran 2 affine registrations of which 2 failed
Ran 0 warp registrations
Reformatted 0 images
logout
Saving session...
...copying shared history...
...saving history...truncating history files...
...completed.

As the reference brain I am using the maximum projection of JRC2018_UNISEX_20x_HR.nrrd.

Any help in explaining me what I could be doing wrong? I would really appreciate it.

Hi, 

I would say align your samples to the template before you apply the projection, the registration command is voxel based and expects 3d geometry.

Dear Jessica,

Sandor is right that you should really be doing the registration in 3D.

However, the proximal problem is that the NRRD header is malformed for one or more of the 2D input images – basically it says that it's a 2D image but then it provides a 3d calibration. I am assuming that you wrote the image from Fiji/ImageJ and this looks like a bug in 

https://github.com/fiji/IO/blob/3a9b1559...

Best,

Greg.

Originally posted by Sandor Kovacs: