[caret-users] afni-caret link error

Donna Hanlon donna at pulvinar.wustl.edu
Tue Jul 6 10:37:09 CDT 2004


Hi Marc,

Sorry for the delayed response; yesterday was a US holiday, so we were 
out of the office.

I get those Unknown Specfile tag messages whenever I open a spec file 
written by SureFit, but they're harmless.  They have nothing to do with 
this problem.  It isn't necessary for the structural volume to be loaded 
in Caret when trying to connect to AFNI.

I'm stumped.  It should work, like it does for me.  What versions of 
caret and AFNI are you running?

The only other explanation for this error I can think of is if 
3dvol_LPI+orig.HEAD's filename has some non-printing characters in it 
that prevent a match with the name in the matrix file.  I've already 
verified that the matrix file's volume name has no non-printing 
characters, but I've seen filename strangeness.  If "ls -l 
3dvol_LPI+orig.HEAD" gives normal output, then we can rule out that 
explanation.

Does the "Unable to find a transformation matrix for 
3dvol_LPI+orig.HEAD" error appear when you do Comm: Connect to AFNI, or 
when you click on a node?

Donna

On 07/05/2004 09:46 AM, Marc Malloy wrote:

>Hi Donna
>
>My matrix file is loaded in caret and the proper volume is selected in AFNI,
>but I still get the same error message.
>I did find this message in the caret terminal window
>
>Unknown SpecFile tag: volume_structural_file
>Unknown SpecFile tag: RAWvtk_file
>Unknown SpecFile tag: FIDUCIALvtk_file
>Unknown SpecFile tag: padded
>Unknown SpecFile tag: investigator
>
>could this have anything to do with it, especially the first line?
>
>marc
>
>----- Original Message ----- 
>From: "Donna Hanlon" <donna at pulvinar.wustl.edu>
>To: "Caret, SureFit, and SuMS software users"
><caret-users at pulvinar.wustl.edu>
>Sent: Friday, July 02, 2004 2:50 PM
>Subject: Re: [caret-users] afni-caret link error
>
>
>  
>
>>Your file looks fine, and it matches the name of a file you had
>>previously uploaded.
>>
>>I can't use your matrix file directly, because I don't have the coord
>>file it cites (or its associated topo file).  But I tried creating a
>>corresponding matrix with a previously uploaded coord file
>>(nov16_2002A_zaps.R.full.segment_vent_corr.fiducial.60744.coord, from
>>which I subtracted the params AC to get an AC-origin version).
>>
>>I had some trouble when I forgot to select the matrix file (easy to do
>>when opening the spec file, since it's not selected by default).  But
>>when I select the matrix; load my spec in caret; start AFNI with
>>yesplugouts; select 3dvol_LPI+orig.HEAD as my anatomy in AFNI (even
>>though this might be selected by default, select it anyway); and open my
>>connection, it works:
>>
>>UNDERLAY /mypath/3dvol_LPI+orig.HEAD
>>
>>AFNI Message: DSET_IJK 110 115 87
>>Voxel highlight: 110 115 87
>>coordinate: 110 115 87
>>AFNI Message: UNDERLAY /mypath/3dvol_LPI+orig.HEAD
>>Found proper transformation matrix
>>Found coordinate file
>>
>>To work properly, though, I had to change -81 to 81 in the second to
>>last line (so all values are positive).
>>
>>The only time I had trouble was where I had a different volume loaded in
>>AFNI or I forgot to select the matrix file when loading the spec.
>>
>>On 07/02/2004 01:19 PM, Marc Malloy wrote:
>>
>>    
>>
>>>file uploaded
>>>
>>>----- Original Message ----- 
>>>From: "Donna Hanlon" <donna at pulvinar.wustl.edu>
>>>To: "Caret, SureFit, and SuMS software users"
>>><caret-users at pulvinar.wustl.edu>
>>>Sent: Friday, July 02, 2004 2:13 PM
>>>Subject: Re: [caret-users] afni-caret link error
>>>
>>>
>>>
>>>
>>>      
>>>
>>>>Marc,
>>>>
>>>>Could you upload your matrix file here:
>>>>
>>>>http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>>>>
>>>>I know you included its contents below, but I want to rule out the
>>>>possibility that there are stray non-printing characters in the version
>>>>you're trying to load.
>>>>
>>>>Donna
>>>>
>>>>On 07/02/2004 01:00 PM, Marc Malloy wrote:
>>>>
>>>>
>>>>
>>>>        
>>>>
>>>>>Hi Donna
>>>>>
>>>>>the matrix file is part of my spec file and I loaded it when I made my
>>>>>
>>>>>
>>>>>          
>>>>>
>>>spec
>>>
>>>
>>>      
>>>
>>>>>file selections.
>>>>>
>>>>>I did File: Open Data File: Volume Comm Matrix right after I created
>>>>>          
>>>>>
>the
>  
>
>>>>>matrix file.
>>>>>
>>>>>marc
>>>>>
>>>>>----- Original Message ----- 
>>>>>From: "Donna Hanlon" <donna at pulvinar.wustl.edu>
>>>>>To: "Caret, SureFit, and SuMS software users"
>>>>><caret-users at pulvinar.wustl.edu>
>>>>>Sent: Friday, July 02, 2004 1:52 PM
>>>>>Subject: Re: [caret-users] afni-caret link error
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>          
>>>>>
>>>>>>Hi Marc,
>>>>>>
>>>>>>Is this matrix in your spec file, and did you load it when made your
>>>>>>spec file selections?
>>>>>>
>>>>>>Or did you do File: Open Data File: Volume Comm Matrix and select the
>>>>>>matrix file?
>>>>>>
>>>>>>Donna
>>>>>>
>>>>>>On 07/02/2004 12:18 PM, Marc Malloy wrote:
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>            
>>>>>>
>>>>>>>I'm attempting to link afni and caret, I've created the matrix file
>>>>>>>              
>>>>>>>
>as
>  
>
>>>>>>>BeginHeader
>>>>>>>date Fri Jul 2 13:02:59 2004
>>>>>>>encoding ASCII
>>>>>>>EndHeader
>>>>>>>tag-transformation-matrix-file-version 2
>>>>>>>tag-number-of-matrices 1
>>>>>>>tag-end-of-tags
>>>>>>>tag-matrix-name local-matrix
>>>>>>>tag-matrix-comment enter comment here
>>>>>>>tag-matrix-target-volume-name 3dvol_LPI+orig.HEAD
>>>>>>>tag-matrix-target-volume-dimensions 72 148 174
>>>>>>>tag-matrix-fiducial-coord-name
>>>>>>>nov16_2002A.L.occipital.segment_corr.marc3.fiducial_AC.56882.coord
>>>>>>>tag-matrix-target-AC-coords 107 131 -81
>>>>>>>tag-matrix-begin
>>>>>>>1.000000 0.000000 0.000000 107.000000
>>>>>>>0.000000 1.000000 0.000000 131.000000
>>>>>>>0.000000 0.000000 1.000000 -81.000000
>>>>>>>0.000000 0.000000 0.000000 1.000000
>>>>>>>
>>>>>>>but each time I try to connect I get this error - Unable to find a
>>>>>>>transformation matrix for 3dvol_LPI+orig.HEAD.
>>>>>>>
>>>>>>>I am viewing  3dvol_LPI+orig in afni, and I have my flat map loaded
>>>>>>>              
>>>>>>>
>in
>  
>
>>>>>>>caret.
>>>>>>>
>>>>>>>marc
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>              
>>>>>>>
>>>>>------------------------------------------------------------------------
>>>>>          
>>>>>
>>>>>>            
>>>>>>
>>>>>>>_______________________________________________
>>>>>>>caret-users mailing list
>>>>>>>caret-users at pulvinar.wustl.edu
>>>>>>>http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>              
>>>>>>>
>>>>>>_______________________________________________
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>>>>>>http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>            
>>>>>>
>>>>>_______________________________________________
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>>>>>http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>          
>>>>>
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>>>>caret-users mailing list
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>>>>
>>>>
>>>>        
>>>>
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>>>
>>>      
>>>
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>>
>>    
>>
>
>
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