NITRC CBS High-Res Brain Processing Tools Forum: open-discussion

RE: CBS tools help on mac 10.10.3

Thomas Ernst — Fri, 27 Jan 2017 13:15:18 GMT

Hi guys,

I had some additional problems in that running the script (version 3.0.8 and 3.0.9) would result in "file not found" errors (MacOS 10.12.3). Finally I figured out that is was the famous "carriage return".

In detail: The original run_cbstools_mac uses two newline characters (carriage return and line feed (CRLF, \r\n)), but MacOS/Unix by default reads the line carriage return character as part of the line text. The nasty bit is: Many editors (like TextEdit) do not show this little detail in the script. Lowest-level solution: remove and retype all newline characters in your editor.

@Pierre: If possible, could you remove the CR characters in run_cbstools_mac the next release please?

RE: Installation Problems

Ian Greenhouse — Fri, 20 Jan 2017 0:06:05 GMT

I am experiencing a similar problem with my installation - MIPAV 7.4.0 running on OSX 10.11.6 and the CBS bundle 3.0.8. I unpacked the .zip bundle and select the .jar files for installation. After clicking the Install Plugin(s) button, about a minute passes before I receive the expected pessimistic message 'No plugins were installed, please select valid MIPAV plugin files.' However, the plugins are not visible in the Plugins menu before or after restarting mipav. The time delay between clicking the install button and receiving the pessimistic message suggests the plugins were installed, but are not appearing in the Plugins menu. Any ideas as to why the plugins may not show up in the menu?

Thanks for any help.

Ian

[UPDATE]
Never mind. I found Kevin Aquino's post below and solved the issue. Thanks anyways.

RE: Installation Problems

Maggie Mae Mell — Tue, 22 Mar 2016 17:34:53 GMT

I just found the included LayoutXML files. Are these what are referenced as the library of standard pipelines?

Thanks again!

RE: Installation Problems

Maggie Mae Mell — Tue, 22 Mar 2016 15:59:10 GMT

Thank you for your response! I think I have it installed properly now.

The documentation I have is named user-guide-r3.0.pdf, in it there is mention of a library of standard pipelines for preprocessing. Are these available somewhere in the jar file or can they be downloaded elsewhere?

Additionally, I am interested in the laminar analysis. I've read the Waehnert paper, but I was wondering if there was any further documentation regarding how to use the software for this type of analysis.

Thank you for your help,

Maggie

RE: Installation Problems

Pierre-Louis Bazin — Tue, 22 Mar 2016 8:10:53 GMT

Hello,

The latest (3.0.8) version of the CBS Tools should work with any release version of MIPAV from 7.0 onward, so far.
You also need a recent JIST version (3.2), conveniently included in the CBS Tools 'bundle'. To install those, just unzip the bundle, start MIPAV, and there select the jar files under 'plugins->install plugins'. No need to uncompress them. Whether you get a positive (plugins installed etc.) or negative ('no plugins installed, select proper file') the files have been installed, and you then just need to select to install the JIST layout tool and process manager from the ~/mipav/plugins directory (if not already installed). Details on this procedure are given in the CBSTools user guide, although the version numbers indicated there are older.
Cheers,

Pilou

Installation Problems

Maggie Mae Mell — Wed, 09 Mar 2016 19:26:52 GMT

Good Afternoon,

I am having issues installing CBS tools. I am running Ubuntu 14.04. I have tried installing both the latest release of MIVAP and an older version, as I noticed your documentation said that newer versions of MIVAP may not work with some Linux distributions. However, I am having the same problem with both versions.

When I try to add the Jar package for CBS tools, my terminal indicates it can't find any of the class files. I know they are there, but it cannot find them within the folders. Is there anything I should be doing to the Jar file before trying to add it?

Please let me know if you need any further information.

Thank you,
MM

Align to mipav space

Kevin Aquino — Thu, 21 Jan 2016 11:42:00 GMT

Hi all,

I am currently using CBS tools and I have noticed in the function "Mesh to Level Set" there is an option to "Align to MIPAV space". Is there a way to undo this transformation in either the scripts or by retrieving the alignment parameters?

Cheers!

RE: CBS tools help on mac 10.10.3

Kevin Aquino — Tue, 22 Sep 2015 14:17:24 GMT

Hi Pierre,

After some searching I found the answer on a blog (can't link it here) - I thought the shell script was called automatically, that was my mistake there.

The missing steps were:

1. Extract all the .jar files to ~/mipav/plugins before installing,
2. Edit the bash script run-cbstools-mac that is within ~/mipav/plugins/ to reflect the correct path.
3. run run-cbstools-mac as a shell script (have to chmod +x run-cbstools-mac it as well)

Optional:
in your .bash_profile you can alias the cbs command via the following:
alias cbstools='source ~/mipav/plugins/run-cbstools-mac'

Cheers!

RE: CBS tools help on mac 10.10.3

Kevin Aquino — Tue, 22 Sep 2015 9:51:55 GMT

Hi Pierre,

Thank you for your reply!

I checked in my plugin directory and it seems that all the files have been unpacked and installed there. However, the plugins are still not recognized.

I edited the paths in the script ~/mipav/plugins/scripts/run-cbstools-mac to be correct for my machine. However, the plugins still do not appear. Is this script run when MIPAV is opened? or has this script have to be executed manually?

Thanks!

RE: CBS tools help on mac 10.10.3

Pierre-Louis Bazin — Tue, 22 Sep 2015 7:16:58 GMT

You may receive a message that "no plugin was installed", even if the installation went well. You can check manually if the tools are there by looking into ~/mipav/plugins/: there should be a 'PlugInJISTLayout.class and a directory tree de/mpg/cbs/

On MacOS, the installation may not be recognized by the usual MIPAV command, so we have also provided some scripts (~/mipav/plugins/scripts/run-cbstools-mac) which should work once you edited the path to use your own user path.