Re: [Freesurfer] Tiger and MNI Linear Register

Eric,

Hi. The MNI Linear Register option is code that is found in the MINC toolkit, and it is that code that is generating the message about not being implemented. So I am afraid you are out of luck in that respect, in that we do not maintain the MINC toolkit. I think our default registration tools do a good job though.

Also, we advocate usage of the command-line tools over csurf, which is a gui that we no longer support. The reason is that it is easier to perform a work-flow from the command-line, and more importantly, it is easier to copy-and-paste any error messages that may appear in a failed run.

You should have a look at the script recon-all. Type:

recon-all --help

This will talk about the processing stages, and is the main 'front-end' to the freesurfer tools.

We will be releasing an online tutorial soon that will fully describe a workflow using recon-all.

Per the message about perl found in your email, freesurfer does use the perl executable installed on the machine, and the MNI tools puts there perl scripts in the path found in the PERL5LIB that freesurfer prints out. That path looks like the /System path I think only because it makes clear which perl version MNI is using.

Nick

On Wed, 2005-08-24 at 14:45 -0500, Yuan-Fen Kuo wrote:

Hi Nick: Thanks for your reply and sorry for my late reply.

 I have checked the "MNI Linear Register" option in the expert  

Preference. When I run "Convert/Average" in "Setup Structural Scan Parameters" I am prompted with the following message "MNI align not yet implemented." in a popped up window. I do all these in the GUI. I did check the log window, and no messages were printed out in there. I have installed the full package ( freesurfer-Darwin-tiger- full.dmg ) with no customization.

 In the previous message I have mentioned my changes to the  

SetUpFreeSurfer.csh script. I have figured out why I did not need to make the modificaitons, however, if you are still interested, I do explain why I made the changes below.

Thank you, Eric

---

 1) I used to un-comment the following lines in  

SetUpFreeSurfer.csh attempting to use the MINC tools ( as modifying the script is usually the first step any tutorial instructs. )

 #setenv MINC_BIN_DIR /usr/pubsw/packages/mni/current/bin
 #setenv MINC_LIB_DIR /usr/pubsw/packages/mni/current/lib

 I realized that these directories do not exist so I changed them to

 MINC_BIN_DIR    /Users/Shared/freesurfer/lib/mni/bin
 MINC_LIB_DIR    /Users/Shared/freesurfer/lib/mni/lib

 then I finally realized that if I do not un-comment the two  

lines in SetUpFreesurfer.csh, the two variables will anyway be set to

 MINC_BIN_DIR    /Users/Shared/freesurfer/lib/mni/bin
 MINC_LIB_DIR    /Users/Shared/freesurfer/lib/mni/lib

 so I have no problem with these two variables now. However,  

perhaps it should be modified in the SetUpFreeSurfer.csh script to avoid confusion?

 2) PERL5LIB is set to

  /Users/Shared/freesurfer/lib/mni/lib/../System/Library/Perl/5.8.6

 while this package is a tiger package, perhaps we can use the  

Perl that comes with Tiger in

 /System/Library/Perl/5.8.6

 I realize in FreeSurferEnv.csh, Tiger's Perl is checked, but it  

is nevertheless set back to

 /Users/Shared/freesurfer/lib/mni/lib/../System/Library/Perl/5.8.6

On Aug 22, 2005, at 3:39 PM, Nick Schmansky wrote:

...

Yuan-Fen,

Hello, I think I need more information before I can diagnose the problem. What is being run when the error message appears? If you could copy and paste the command-line output, that would be helpful.

Also, I am not sure what was changed in the SetUpFreeSurfer.csh script, as the MINC_BIN_DIR and MINC_LIB_DIR vars are correct (and are the default). What were they set to prior?

Thanks,

Nick

On Mon, 2005-08-22 at 14:50 -0500, Yuan-Fen Kuo wrote:

...

Hi.

I have installed the freesurfer-Darwin-tiger-full.dmg

and I would like to use the MNI Linear Register option.

I have been prompted that "MNI has not been align not yet implemented."

Because of this message, I have changed my SetUpFreeSurfer.csh script so that the following directories are pointed to the corresponding path instead of the default that came with the package.

MINC_BIN_DIR /Users/Shared/freesurfer/lib/mni/bin MINC_LIB_DIR /Users/Shared/freesurfer/lib/mni/lib PERL5LIB /System/Library/Perl/5.8.6

However, I still get the same message.

Is there something I am missing?

Thanks in advance. Eric _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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