Mrview error: unknown option

Hello!

I have a quick question! I have been trying to visually inspect the output of the different pre-processing steps using mrview and I get the following error:
mrview: unknown option "-roi.load"
mrview: unknown option "-odf.load_shd"
mrview: unknown option "-tractography.load"
Any advice would be much appreciated.

Cheers,
Vasiliki

Hello Vasiliki,

“-odf.load_shd” should be “-odf.load_sh”

Are you using the latest version of mrtrix? You can see the options for your version of mrview with mrview -help.

Hi Max,

Oh yes, I am sorry, that was a typo.

I think I have the latest version. I am using the version we installed about a month ago.

Is there any chance that mrview version is older or has not been installed appropriately?

I checked mrview -help previously but none of these options appeared.

Cheers,
Vasiliki

You might have multiple mrview in your path as these options existed for quite some time.

I suspect your current mrview lives in ~/mrtrix3/release/bin/mrview. Check that the path of which mrview matches that one. If not you’ll need to edit your PATH variable presumably in .bash_profile or .bashrc. You can check your PATH with echo $PATH.

You can find out your version with mrview --version. The latest is mrview 0.3.15-222.

Hi Max,

I think I am having the same problem here because I don’t get these options . I checked my path and it is /Applications/mrtrix-0.2.12/bin:/applications/mrtrix3/bin:/usr/local/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin

Is this wrong? Can you please help me to fix it?
Thank you!

You are using a very old version of mrtrix. Did you install mrtrix3 on your system?

Hi max,

Thanks for such a quick response! Yes I have mrtrix3 installed on this computer as well. In my applications folder I have mrtrix-0.2. 12 and mrtrix3
I’m guessing I did something wrong with the installation? We had to trade computers here a while ago so when I took over this Mac I loaded in my user profile… I wonder if that caused the problem? How do I fix it?

Assuming mrtrix3 is installed in /Applications/MRTRIX3, which contains a release and script folder:

does the folder contain a file called set_path? If so, follow these instructions and ignore the rest of this message.

If not, then the following (executed in the same terminal) should give you the path and version of mrview from your mrtrix3 installation:

PATH=/Applications/MRTRIX3/release/bin:/Applications/MRTRIX3/scripts:$PATH
which mrview
mrview --version

When that works you might want to make it persistent. This

echo "export PATH=/Applications/MRTRIX3/release/bin:/Applications/MRTRIX3/scripts:$PATH" >> ~/.bash_profile

OR this

echo "export PATH=/Applications/MRTRIX3/release/bin:/Applications/MRTRIX3/scripts:$PATH" >> ~/.bashrc

should do the trick.

Okay I have followed yoiur instructions, I did the “if not” version. Here is a screen shot of the terminal…

When I now type mrview -help I still do not see the options for -roi.load

I also get this now when I open a new terminal

Sorry for the multiple replies…

As way too often, the error is in the first line :wink: and error message appears because of a typo I had in the export statements: it should be export PATH=... not export $PATH=...

To fix it, remove the last line(s) in ~/.bashrc and ~/.bash_profile that contain referrnces to /Applications/MRTRIX3.

Then, type
echo "export PATH=/applications/mrtrix3/bin:/applications/mrtrix3/scripts:$PATH" >> ~/.bash_profile
open a new terminal and type
`echo $PATH".

/applications/mrtrix3/bin should be the first entry in your PATH (or at least before /Applications/mrtrix-0.2.12). If not then we need to find out where your PATH is modified after sourcing .bash_profile.

Can we back up a step and can you please tell me how do I get to or find ~/.bashrc and ~/.bash_profile ? I am not at all very savy with these things…

No problem: open ~/.bash_profile should open a text editor. If not, open -a TextEdit ~/.bash_profile should work.

Thanks, so when I do this I have all of this text show up:
export /Applications/mrtrix-0.2.12/bin:/applications/mrtrix3/bin:/usr/local/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin=/Applications/MRTRIX3/release/bin:/Applications/MRTRIX3/scripts:/Applications/mrtrix-0.2.12/bin:/applications/mrtrix3/bin:/usr/local/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin

mrtrix3 is referenced 3 times - how much of this do I erase?

Is this the content of ~/.bash_profile or what echo $PATH gives you?

If this is in ~/.bash_profile, change it to:

export PATH=/applications/mrtrix3/bin:/applications/mrtrix3/scripts:/Applications/mrtrix-0.2.12/bin:/usr/local/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin

if not:
post the ouput of
cat ~/.bash_profile

Okay so I have done that in the ~/.bash_profile and when I do cat ~/.bash_profile now I get:
bash-3.2$ cat ~/.bash_profile
export PATH=/applications/mrtrix3/bin:/applications/mrtrix3/scripts:/Applications/mrtrix
export PATH=/applications/mrtrix3/bin:/applications/mrtrix3/scripts:/Applications/mrtrix-0.2.12/bin:/applications/mrtrix3/bin:/usr/local/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin

Is this okay? Is it all fixed now?
Thank you so much for being so patient with me!!

Actually, the line you posted is entirely consistent with the typo mentioned earlier: export $PATH=... would have substituted the whole path rather than assigning to PATH. @Jhodge, you want to delete that line, and use the new set_path script, which we added a few months ago to simplify this process - see instructions on installation page. That should sort things out properly - but you do need to remove the mess created by earlier attempts in the files @maxpietsch mentioned before proceeding…

Okay so I did cd /Applications/mrtrix3 and then ./set_path and got this error…

ERROR: MRtrix3 executables not found in expected location.

This script needs to be run from within the MRtrix3 toplevel directory, AND
after the build script has successfully completed. In addition, the set_path
script should NOT be moved from its original location in the MRtrix3 toplevel
directory.

Sorry for the trouble but I think we are nearly there. Be careful with paths as they are case sensitive:
You mention /Applications/mrtrix3 and /applications/mrtrix3.

set_path checks whether there is a directory called release in the same folder. This should be the case for the latest mrtrix3 and default installation but your installation might differ.

To fix your problem, just remove the (fist) line in .bash_profile:

so that the following line remains:

export PATH=/applications/mrtrix3/bin:/applications/mrtrix3/scripts:/Applications/mrtrix-0.2.12/bin:/usr/local/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin:/usr/local/fsl/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/opt/X11/bin