Biorad Writer plug-in for brain registration with cmtk GUI

[Huayi Wei]

Hi Gregory,

I'm trying to use the fiji CMTK GUI to register some of my nc-82 stained brains. I was referring to the protocol: http://cshprotocols.cshlp.org/content/2013/4/pdb.prot071738.full . It asks for converting all images into the Biorad format with the Biorad Write plug-in. However, I could no longer find it by googling. Do you have the plug-in available for download somewhere? Or it's no longer necessary to convert the files?

Cheers

Huayi 

[Gregory Jefferis]

Dear Huayi Wei,

I am afraid that aspect of the protocol is out of date. We now use the nrrd format exclusively. You can save your images as nrrd with Fiji. The folder organisation and file naming conventions remain the same except that image files should end in nrrd not pic. Note that you may wish to save nrrds in compressed format by holding down the Alt key before choosing the relevant menu item.

Best,

Greg. 

Sent from my iPhone

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[Gregory Jefferis]

As an aside the Biorad_Writer plugin source code (which can be compiled and installed via the ImageJ Plugins menu is still available at:

https://imagej.nih.gov/ij/plugins/download/misc/Biorad_Writer.java

Furthermore the standard version of Fiji comes with this plugin via the VIB protocol plugin

https://github.com/fiji/VIB/blob/master/src/main/java/Biorad_Writer.java

so you can choose do File ... Save as Biorad ... in Fiji.

Best wishes,

Greg. 

On 18 Jan 2017, at 23:18, Huayi Wei <hw1...@nyu.edu> wrote:

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Gregory Jefferis, PhD

Division of Neurobiology

MRC Laboratory of Molecular Biology

Francis Crick Avenue

Cambridge Biomedical Campus

Cambridge, CB2 OQH, UK

http://www2.mrc-lmb.cam.ac.uk/group-leaders/h-to-m/g-jefferis

http://jefferislab.org

http://flybrain.stanford.edu

[Huayi Wei]

Thanks Greg. I found the new tutorial on CMTK GUI. So I followed it & tried it out on both Windows 10 & Fedora. But I always get this error:

Traceback (most recent call last):
  File "CMTK_Registration/CMTK_Registration_GUI.py", line 211, in <module>
  File "CMTK_Registration/CMTK_Registration_GUI.py", line 211, in <module>
  File "/home/huayi/Programs/Fiji.app/plugins/CMTK_Registration/cmtkgui.py", line 97, in makescript
    os.chmod(filepath,0755)
OSError: [Errno 20000] Unknown error: 20000: u'/home/huayi/Desktop/Nat_test/commands/munger_2017-01-19_12.39.57.sh'

And the file that generated in the 'commands' folder would be a .sh file that wouldn't run either through Cygwin(windows) or fedora terminal. The content as:

#!/bin/sh
# 2017-01-19_12.39.57
cd "/home/huayi/Desktop/Nat_test"
"/home/huayi/Programs/Fiji.app/bin/cmtk/munger" -b "/home/huayi/Programs/Fiji.app/bin/cmtk" -a -w -r 010203  -X 26 -C 8 -G 80 -R 4 -A '--accuracy 0.4' -W '--accuracy 0.4'  -T 2 -s "refbrain/NCD6RLH-rev_raw01.nrrd" images

I can't quite understand what might be wrong.
Huayi

[Gregory Jefferis]

On 19 Jan 2017, at 17:56, Huayi Wei <hw1...@nyu.edu> wrote:

> Thanks Greg. I found the new tutorial on CMTK GUI. So I followed it & tried it out on both Windows 10 & Fedora. But I always get this error:
>
> Traceback (most recent call last):
> File "CMTK_Registration/CMTK_Registration_GUI.py", line 211, in <module>
> File "CMTK_Registration/CMTK_Registration_GUI.py", line 211, in <module>
> File "/home/huayi/Programs/Fiji.app/plugins/CMTK_Registration/cmtkgui.py", line 97, in makescript
> os.chmod(filepath,0755)
> OSError: [Errno 20000] Unknown error: 20000: u'/home/huayi/Desktop/Nat_test/commands/munger_2017-01-19_12.39.57.sh'

This is a bug in the jython distributed. It is very annoying but there is nothing I can do about it. That said it can be ignored. I think it relates to making the .sh script executable.

> And the file that generated in the 'commands' folder would be a .sh file that wouldn't run either through Cygwin(windows) or fedora terminal. The content as:
>
> #!/bin/sh
> # 2017-01-19_12.39.57
> cd "/home/huayi/Desktop/Nat_test"
> "/home/huayi/Programs/Fiji.app/bin/cmtk/munger" -b "/home/huayi/Programs/Fiji.app/bin/cmtk" -a -w -r 010203 -X 26 -C 8 -G 80 -R 4 -A '--accuracy 0.4' -W '--accuracy 0.4' -T 2 -s "refbrain/NCD6RLH-rev_raw01.nrrd" images

Why do you say this script does not run? What happens if you run

sh /path/to/my/mungerscript.sh

? Is there an error message?

Best,

Greg.

[Huayi Wei]

Hi Greg,
Here's what I got on Fedora.

sh munger_2017-01-19_12.39.57.sh
munger_2017-01-19_12.39.57.sh: line 4: /home/huayi/Programs/Fiji.app/bin/cmtk/munger: No such file or directory

h

[Gregory Jefferis]

On 19 Jan 2017, at 18:10, Huayi Wei <hw1...@nyu.edu> wrote:

> Hi Greg,
> Here's what I got on Fedora.
>
> sh munger_2017-01-19_12.39.57.sh
> munger_2017-01-19_12.39.57.sh: line 4: /home/huayi/Programs/Fiji.app/bin/cmtk/munger: No such file or directory

That means that CMTK is not installed. Did you run the menu item to install it?

best,

[Huayi Wei]

Hi Greg,

So now I have installed. I could see all the files under bin/cmtk. But here's what I got when I run the code, through cygwin on windows:

$ sh munger_2017-01-19_17.12.38.sh

: No such file or directorysh: line 3: cd: C:\Users\Huayi\Google Drive\Nat_Test

munger_2017-01-19_17.12.38.sh: line 4: C:\Fiji.app\bin\cmtk\munger: command not found

I could see the munger file under the cmtk folder. Maybe this is a problem related to indexing directories? 

huayi

[Greg Jefferis]

Hi Huayi,

Can you send a recursive directory listing of the C:\Fiji.app\bin folder? Or just zip it up and send to me offlist. Best,

Greg.

[Gregory Jefferis]

Dear Huayi,

I looked at the contents of the C:\Fiji.app\bin that you sent me off list.

Everything seems to be in the correct place. My impression is that the problem is with the paths. Are you running this script from inside a cygwin shell? Unfortunately I almost never use windows or cygwin so I forget if they will cope with both windows and unix style paths. The paths that are giving errors (lines 3 and 4 of your script) are Windows paths. I think you could try quoting the paths. 

By default cmtk gui writes scripts with double quotes around the paths. I think this may not work for windows paths in the cygwin shell. Do you want to try changing the double quotes to single quotes and seeing if that helps e.g. change:

cd "C:\Users\Huayi\Google Drive\Nat_Test"

to 

cd 'C:\Users\Huayi\Google Drive\Nat_Test'

Best wishes,

Greg.

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