Hi Guys,

I am a novice CMTK user using the fiji GUI. To start optimising my registration parameters Ii would like to see the reformatted images between steps. So to see the image after afine registration and the final image after warping.  I have adapted the command file to the following:

"/Users/SiegerLab/Desktop/Fiji.app/bin/cmtk/munger" -b "/Users/SiegerLab/Desktop/Fiji.app/bin/cmtk" -a -w -r 010203 -l fpa -T 24 -s "refbrain/refbrain.nrrd" images

Which I thought would give me the reformatted image after principal axis alignment(p), affine(a) and the final(f) image. However, when i ran the protocol none of my images where reformatted. The log showed me the following list

Ran 0 initial affine registrations of which 0 failed
Ran 2 affine registrations of which 0 failed
Ran 2 warp registrations
Reformatted 0 images
logout

[Process completed]

It would be great if one of you guys could tell me how come my output doesn't include the reformatted images.  

I will be grateful for any help you can provide.

Cheers,

Pieter

Dear Pieter,

This problem is almost certainly specific to the munger script that I wrote. munger is distributed with CMTK but not really a core part of CMTK.

In terms of your problem, the command line looks sensible to me. We will need some more information. You can try running the reformatting with affine and final only and adding a verbose switch to see if it gives more information:

since there is no principal axis alignment being used here and the standard log message is not that informative.

There are situations where reformatting fails because of some specific requirements for the image file names (they need to have the channel number at the end formatted as 01 02 03 etc e.g. myimg1_01.nrrd myimg1_02.nrrd myimage2_01.nrrd myimage2_02.nrrd etc), but then you would not have any output images in your reformatted directory at all.

Best wishes,

Greg.

Hi greg,

Thank you for the quick and helpful reply. I don't think the problem is the file names. If i use the GUI to generate a command file without changing any parameters I get reformatted images. It is specifically when i start changing stuff that this problem occurs.

So i did as you suggested, I ran the registration again with affine and final only. Also this time i don't get any actual reformatted images as output.

The command i ran this time was

"/Users/SiegerLab/Desktop/Fiji.app/bin/cmtk/munger" -b "/Users/SiegerLab/Desktop/Fiji.app/bin/cmtk" -a -w -r 010203 -l af -v -T 24 -s "refbrain/refbrain.nrrd" images" 

The output consisted of a folder named registration containing the affine and warp lists.  

The output in the terminal (the last bit) was:

Found brain name WT one_01 (images/WT one_01 .nrrd)
New working directory is: /Volumes/User Data 3 6TB/Pieter/LSM data /02062016/test/rigid registration test/yourregistrationfolder copy, Old one was /Volumes/User Data 3 6TB/Pieter/LSM data /02062016/test/rigid registration test/yourregistrationfolder copy/images
inlist = Registration/affine/refbrain_WT one_01 _9dof.list
W: outlist = Registration/warp/refbrain_WT one_01 _warp_m0g40c4e1e-1x16r3.list
outdir exists
Reformat:inlist would be: Registration/affine/refbrain_WT one_01 01_9dof.list
Reformat:inlist would be: Registration/warp/refbrain_WT one_01 01_warp_m0g40c4e1e-1x16r3.list
Found brain name WT one_02 (images/WT one_02 .nrrd)
New working directory is: /Volumes/User Data 3 6TB/Pieter/LSM data /02062016/test/rigid registration test/yourregistrationfolder copy, Old one was /Volumes/User Data 3 6TB/Pieter/LSM data /02062016/test/rigid registration test/yourregistrationfolder copy/images
inlist = Registration/affine/refbrain_WT one_02 _9dof.list
W: outlist = Registration/warp/refbrain_WT one_02 _warp_m0g40c4e1e-1x16r3.list
outdir exists
Reformat:inlist would be: Registration/affine/refbrain_WT one_02 01_9dof.list
Reformat:inlist would be: Registration/warp/refbrain_WT one_02 01_warp_m0g40c4e1e-1x16r3.list

Ran 0 initial affine registrations of which 0 failed
Ran 2 affine registrations of which 0 failed
Ran 2 warp registrations
Reformatted 0 images
logout

Any suggestions are most welcome!

Best,

Pieter

Hi Pieter,

Could you check your input image file names. It looks like there are spaces in the name (which is strongly discouraged)

"WT one_01 .nrrd"

and in particular that there is a space between _01 and .nrrd which could be the source of the problem.

Best wishes,

Greg.