Convert3D in command line

[Christopher Finuf]

I was successful in making the download but when I go to use it in the terminal I get the error:

Christophers-MacBook-Pro:~ BrainImage$ c3d -verbose n4.nii.gz -resample-mm 1x1x1mm -o t1_resampled.nii.gz

-bash: c3d: command not found

How can I get it to work in the terminal?

[Paul Yushkevich]

When you download Convert3D from sourceforge, and double click the installer, it should open a window that has a folder called usr_local_bin and also items c3d c2d c3d_affine_tool. Drag these items into the folder. Then you should be able to use the commands from the terminal.

Or you can use the GUI. 

Paul

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Paul A. Yushkevich, Ph.D.
Associate Professor
Penn Image Computing and Science Laboratory
Department of Radiology
University of Pennsylvania

[Brett Marinelli]

I'm also trying to work from the terminal command line so that I can more easily batch convert (didn't see anything on how to make loops from within the cd3 GUI).

However, I can't find the usr_local_bin folder that you mention. After downloading the .dmg for Mac it just has be drag "Conver3DGUI" into "Applications".

Am I missing something?

Thanks!

Brett

[Paul Yushkevich]

Brett,

I don't know what happened to the installer script, but you are absolutely right, the command line binaries don't show up. Here is the work-around:

1. Right-click on the Convert3DGui.app and select "Show Package Contents"

2. Open the Contents/bin folder

3. Copy the contents to /usr/local/bin (using terminal, or in Finder using Command-Shift-G to open the folder).

I'll dig around when I get a chance.

Paul.

[xiao.xia...@gmail.com]

Hi Paul, 

May know whether is there any updates for this issue.

I  am trying to install the Convert3D on the MacOS, however, there is no bin folder under the path: /Applications/Convert3DGUI.app/Contents/bin

May I know is there any other options to use it in the terminal.

Thanks,

Xiaoqian  

[Paul Yushkevich]

I have no idea why the bin folder is missing. Try removing Convert3DGUI from the Applications folder and reinstalling. If that does not work, install the Experimental build of ITK-SNAP from the sourceforge download page for ITK-SNAP. The new ITK_SNAP build includes the c3d binary. There are instructions under the Help menu on how to install.

Thanks!
Paul

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[xiaoqian xiao]

Thanks Paul,

Install the ITK-SNAP works for me.

Best,

Xiaoqian