Hi all, I'd like to help non-coders learn how to use CMTK, but it's been a few years since I've used it myself. Is the Fiji CMTK GUI the best way to go? Its instructions at https://github.com/jefferis/fiji-cmtk-gu... rely on Fiji's "update sites", but the latest Fiji doesn't seem to have that type of updater. The instructions' link to the Jefferis Lab Wiki also seems to be down. If there are up-to-date protocols for installation and basic use for non-coders (or at least explicit instructions for people new to command lines), could someone please point me to them? Thank you!

Hi Claire,

I didn’t realise that the update sites no longer work with Fiji. The current Fiji plug-in can work without them but actually I’d suggest that you take a look at:

https://github.com/sandorbx/Parallel-Fij...

Sandor Kovacs is signed up to the list and may have more to add. I need to get our wiki visible again when I’m back. All the best,
Greg.

Originally posted by c_mckellar:
FWIW, if you are looking for instructions on how to use the command lines of some essential CMTK tools directly, there is a "User Guide" in the "Documents" section here on NITRC: https://www.nitrc.org/docman/index.php?group_id=212&selected_doc_group_id=710&language_id=1#folder

PDF is attached for convenience.

Best,
  Torsten

Thanks, I did glance through that User Guide but I don't think there are any sections in it that would help a non-coder. Here's how explicit I'm trying to make the instructions to align fly brains, below. I haven't been able to find any instructions for the CMTK interface in Fiji, since the link to the flybrain wiki is down. Haven't been able to get CMTK to work from Fiji, myself. Using the "Registration Parameter Preset" of the full brain and changing no other settings, the Log just says "Registration warp failed, Registration affine failed." So I currently only wrote pre-prep instructions:

Here's the type of thing I'm trying to write:
Follow the instructions at:
https://github.com/sandorbx/Parallel-Fij...
(This will require typing a few things into a command line but don't worry if you're not a coder, it will tell you what to do).
For the part that requires Ubuntu, note that it must be installed through the Microsoft Store, which can have problems if not recently updated through Windows Updates. Update, then reboot your computer.
When the instructions refer to the file named "Parallel_Fiji_CMTK_Registration***.ijm", that comes from a collection of files from the green "Code" button at the top of the instructions page. Download the ZIP then extract it, and move the relevant .ijm file for your operating system as outlined in the instructions.
If your confocal stack is not already separated out into different files for different channels, open it in Fiji. Scroll to a slice where you can see the brain.
>Image >Transform >Rotate >Check "Preview" >Change angle until brain is upright
Draw a box around brain but not too tightly
>Image >Crop
>Image >Color >Split channels
Select the nc82 reference channel image
>Save >NRRD >remove the leading characters that Fiji inserts, and give it a name ending in _01
Select the neuron stain image (e.g. GFP)
>Save >NRRD >choose exactly the same name as the reference image, but ending in _02
Check the FlyWire Gateway to see what template brains that site can work with, then download an appropriate one from:
https://www.janelia.org/open-science/jrc...
To run alignment in Fiji: >Plugins >Macros >Parallel Fiji CMTK Registration...

Hi, Lets just try to run CMTK and the Fiji GUI on your setup first, Probably I should add this to the readme but your problem could be that there is a space or a special character in any of the file paths, if not  can you tell me which operating system you want to use ?

 I think Torsten's guide is very useful when you use it while exploring CMTK in the command line, for example running the "cmtk --help" command, you can add the help options to any command to see what kind of operations and parameters you can use and what is the basic syntax, you can even find some basic explanations there. I encourage you to actually try the examples in the userguide, while reading the help pages, and experimenting with the options. CMTK real challange that it requires some understanding of the underlying image mathematics for effective use, coding is really just typing in the commands following the syntax on the help pages, maybe add some basic logic combining it with bash commands.



Originally posted by c_mckellar:

Thanks for the reply! I'm using Windows 10. It would be great to have your help; how would we check whether it's just a problem with the file paths?

To check the file paths start the macro in Fiji, and take a look at the file paths under the "Input&Output options", if its empty choose the locations with the browse button first. For example for reference image it looks something like this , depending on where is yours   "C:\Users\admin\test_data\refbrain\JRC2018_UNISEX_20xHR.nrrd" , now check if there is any space character there, if yes change the folder or file name using your file explorer to do not contain spaces, then in the macro browse for the file or folder again before you run it. 

If further troubleshooting is needed use this test data

 https://www.dropbox.com/sh/54igm0xxmtlo4ei/AAA7EpGMZcoN_CMs8kG8zI26a?dl=0

-place test_data folder  on one of your internal hard drives directly like "C:\test_data" , use the images and the reference provided to run a registration.

-confirm that CMTK installed, open ubuntu terminal and type the command cmtk --help , after hitting enter you should see the cmtk help page.

- on windows 10 the macro has the limitation that it can just read files on the internal hard drives and not from network or external drive locations

Hope this will help.

Thanks very much for your help, the issue was solved by removing spaces from the file paths! For posterity, here are basic instructions compiled for non-coders to install CTMK and align fly brains, with sections from your replies if that's okay:

Follow the instructions at:
https://github.com/sandorbx/Parallel-Fij...
(This will require typing a few things into a command line but don't worry if you're not a coder, it will tell you what to do).
Where it says for Windows, "Start powershell as admin", do the following:
Press Windows+R to open Run, and then type "powershell" in the text box but don't press Okay, press Ctrl+Shift+Enter.
For the part that requires Ubuntu, note that it must be installed through the Microsoft Store, which can have problems if not recently updated through Windows Updates. Then reboot your computer. https://www.microsoft.com/en-us/p/ubuntu...
When the instructions refer to the file named "Parallel_Fiji_CMTK_Registration***.ijm", that comes from a collection of files from the green "Code" button at the top of the instructions page. Download the ZIP then extract it, and move the relevant .ijm file for your operating system as outlined in the instructions.
If your confocal stack is not already separated out into different files for different channels, open it in Fiji. Scroll to a slice where you can see the brain.
>Image >Transform >Rotate >Check "Preview" >Change angle until brain is upright
Draw a box around brain but not too tightly
>Image >Crop
>Image >Color >Split channels
Select the nc82 reference channel image
>Save >NRRD >remove the leading characters that Fiji inserts, and give it a name ending in _01. Make sure there are no white spaces anywhere in the file path or name. On windows 10 the macro has the limitation that it can just read files on the internal hard drives and not from network or external drive locations.
Select the neuron stain image (e.g. GFP)
>Save >NRRD >choose exactly the same name as the reference image, but ending in _02
Check the FlyWire Gateway: https://flywiregateway.pniapps.org/ to see what template brains that site can work with, then download an appropriate one from:
https://www.janelia.org/open-science/jrc...
To run alignment in Fiji: >Plugins >Macros >Parallel Fiji CMTK Registration.
Choose an operation: Affine & warp registration
Registration parameter preset: Full Flybrain
Select desired output directory (no spaces in path names), template brain location & output directory.
Check "Show results list" and check "Reformat channel 01, 02, 03"
In the Log window, scroll to the bottom to see if it's running ("Please wait")
After a period of time (that can take quite a while), the aligned files will appear as stacks in the output directory you selected.
If troubleshooting is needed use this test data:
https://www.dropbox.com/sh/54igm0xxmtlo4...
-Place test_data folder on one of your internal hard drives directly like "C:\test_data" , use the images and the reference provided to run a registration.
-confirm that CMTK installed, open ubuntu terminal and type the command cmtk --help , after hitting enter you should see the cmtk help page.

I'm glad that it works now, instructions are looking good. 

Maybe using the skip final resolution option can be useful for home computers, especially with high res samples, the registration quality is not affected negatively usually, and the compute time can be considerably faster.

If this is for teaching material I'm happy to give more feedback on it or offer additional help, just write me an email.

Thanks, Sandor! This is indeed for teaching purposes, in that I'm trying to provide resources for fly labs who use our FlyWire platform. I'd be happy to accept any additional input or edits to the instructions! If we do it here, rather than by email, then CMTK forum users will also have your guidance. : )

Hello - I am new to this forum and toolset and very grateful for you for putting together this instruction set.  I followed the instructions and was able to install the macro for FIJI (Parallel FIJI CMTK Registration Mac20 on my mac), but I am getting an error with no reformatting (see below for details) even when I use the test dataset linked from the dropbox earlier in this thread.  I have no coding experience, so I think I am the type of person you wrote these instruction for and I'd very much appreciate your help in getting te fly brain registration to work for me.  Thank you so much

result from running macro:

Started Affine and Warp Registration on 1 samples
Preset: Full Flybrain(Cachero-Ostrovksy_2010)
 
Affine parameters:
Initial affine method: --centers-of-mass
Affine registration metric: Normalized Mutual Information
Exploration [Initial optimizer step size]: 16
Accuracy [Final optimizer step size]: 0.8
Degrees of freedom first pass: 6
Degrees of freedom second pass: 9

Warp parameters:
Warp registration metric: Normalized Mutual Information
initial exploration step size: 26
Accuracy [Final exploration step size]: 0.4
coarsest resampling: 8
Refine grid: 4
grid size: 80
 
Job list:
gehirn
(cmtk make_initial_affine --centers-of-mass /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/images/gehirn_01.nrrd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_init.list; cmtk registration --initial /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_init.list --nmi --dofs 6 --dofs 9 --nmi --exploration 16 --accuracy 0.8 --omit-original-data -o /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_affine.xform /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/images/gehirn_01.nrrd; cmtk warp --nmi --threads 160 --jacobian-weight 0 --fast -e 26 --grid-spacing 80 --energy-weight 1e-1 --refine 4 --coarsest 8 --ic-weight 0 --accuracy 0.4 --omit-original-data -o /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_warp.xform /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_affine.xform;cd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8; cmtk reformatx --pad-out 0 -o Reformatted/warp_gehirn_01.nrrd --floating /Users/meilinwu/Desktop/test/images/gehirn_01.nrrd /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_warp.xform & cd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8; cmtk reformatx --pad-out 0 -o Reformatted/warp_gehirn_02.nrrd --floating /Users/meilinwu/Desktop/test/images/gehirn_02.nrrd /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_warp.xform & cd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8; cmtk reformatx --pad-out 0 -o Reformatted/warp_gehirn_03.nrrd --floating /Users/meilinwu/Desktop/test/images/gehirn_03.nrrd /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_warp.xform ) & 
 
Please wait
(cmtk make_initial_affine --centers-of-mass /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/images/gehirn_01.nrrd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_init.list; cmtk registration --initial /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_init.list --nmi --dofs 6 --dofs 9 --nmi --exploration 16 --accuracy 0.8 --omit-original-data -o /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_affine.xform /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/images/gehirn_01.nrrd; cmtk warp --nmi --threads 160 --jacobian-weight 0 --fast -e 26 --grid-spacing 80 --energy-weight 1e-1 --refine 4 --coarsest 8 --ic-weight 0 --accuracy 0.4 --omit-original-data -o /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_warp.xform /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_affine.xform;cd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8; cmtk reformatx --pad-out 0 -o Reformatted/warp_gehirn_01.nrrd --floating /Users/meilinwu/Desktop/test/images/gehirn_01.nrrd /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_warp.xform & cd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8; cmtk reformatx --pad-out 0 -o Reformatted/warp_gehirn_02.nrrd --floating /Users/meilinwu/Desktop/test/images/gehirn_02.nrrd /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_warp.xform & cd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8; cmtk reformatx --pad-out 0 -o Reformatted/warp_gehirn_03.nrrd --floating /Users/meilinwu/Desktop/test/images/gehirn_03.nrrd /Users/meilinwu/Desktop/test/refbrain/JRC2018_UNISEX_20xHR.nrrd /Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/gehirn_warp.xform ) &  wait;
execution time was 0 s.
 
gehirn Registration warp failed
gehirn Registration affine failed
Reformat failed:/Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/Reformatted/warp_gehirn_01.nrrd
Reformat failed:/Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/Reformatted/warp_gehirn_02.nrrd
Reformat failed:/Users/meilinwu/Desktop/test/result/gehirn_Registration_2026-1-13-13-8/Reformatted/warp_gehirn_03.nrrd
 
Reformatted 0 images

 

Hello - I am late to the game and very much a non-coder, but would really love to be able to register my fly brain images for use with platforms like Flywire.  I followed the instructions above to install the FIJI plugin and it looked like it installed properly, but gives an error when I try the registration even with the test data provided above.  I am at a loss as to how to move forward and was hoping for some guidace from the experts on this forum.  Any advice would be greatly appreciated!!

 

Hi,  thanks for the interest, was a long time I tested this on a mac, not even sure if bash commands like this are still working in the current shell. I will get back to you as soon as I figure it out. 

Hi Sandor - thank you so much for taking the time to help me with this.  Not sure if it is relevant, but I'm using a 5yr old macbook pro running macOS15.6.1.  Processor is 2.4GH 8-core intel i9 with 32GB RAM.  I was wonding if maybe the processor is not sufficiently powerful?  

That should be sufficient, also good news that its an Intel chip, for the Apple silicon you would need Rosetta or an ARM build. In the meantime maybe you can confrim if you have a working CMTK install by running "cmtk --help" command in the terminal, or try some examples from the CMTK userguide :https://insight-journal.org/browse/publication/706/#manuscript

Sorry if this is posted multiple times, for some reason it doesn't seem to be showing up.  

Thank you for the suggestion.  When I enter that command, the response is:

-bash: cmtk--help: command not found

Does this mean the installation failed?  I do believe something was installed because I can access the cmtk plugin in FIJI (see attachment) 

Originally posted by mwu:

-bash: cmtk--help: command not found

 

Maybe this is just a typo in your post, but to be sure - there needs to be a space between `cmtk` and `--help` :)

Thanks!  I wasn't sure so I did it with and without the space and got the same response. 

Macintosh-62:~ meilinwu$ cmtk --help

-bash: cmtk: command not found

Macintosh-62:~ meilinwu$ cmtk--help

-bash: cmtk--help: command not found

I'm guessing that is not a good sign for me...