[caret-users] Re: node size control

David Van Essen vanessen at pulvinar.wustl.edu
Fri Jul 9 14:29:52 CDT 2004


Another partial work-around is to reduce the node size (D/C: Surface  
Miscellaneous: Node Size) to its current minimum of 1 mm instead of the  
default of 2.  This won't eliminate the node (unless/until John allows  
this to be set to 0) but it does make the nodes much less obtrusive.

DVE


On Jul 9, 2004, at 2:11 PM, John Harwell wrote:

>
>
> On Jul 9, 2004, at 1:46 PM, Marc Malloy wrote:
>
>> Hi John
>>
>> Sorry, what I meant was is it possible to have just the crosshairs  
>> identify
>> the node when you click on one, not both the crosshairs and the
>> identification squares.  Thanks.
>>
>
> Not at this time.  Each time you identify a node, the green square  
> will appear.  You can also remove the green identify square by press  
> the CID button on the Identify Dialog that pops up when you identify a  
> node.
>
>> marc
>>
>> ----- Original Message -----
>> From: "John Harwell" <john at pulvinar.wustl.edu>
>> To: "Caret, SureFit, and SuMS software users"
>> <caret-users at pulvinar.wustl.edu>
>> Sent: Friday, July 09, 2004 2:40 PM
>> Subject: Re: [caret-users] afni-caret link error
>>
>>
>>>
>>> Hi Marc,
>>>
>>> Use Surface Menu: Identify: Clear Node Identify Symbols to remove any
>>> displayed identification squares.
>>>
>>> ----------------------------------------------------------
>>> John Harwell
>>> john at pulvinar.wustl.edu
>>> 314-362-3467
>>>
>>> Department of Anatomy and Neurobiology
>>> Washington University School of Medicine
>>> 660 S. Euclid Ave.    Box 8108
>>> St. Louis, MO 63110   USA
>>>
>>> On Jul 9, 2004, at 1:18 PM, Marc Malloy wrote:
>>>
>>>> Hi Donna
>>>>
>>>> Sorry for the belated response.
>>>>
>>>> I'm running caret5 on RedHat 9 through Exceed 3D 9.0.
>>>>
>>>> Is there a way to turn off the square that identifies a node when  
>>>> you
>>>> click
>>>> on it?  It obstructs the activation that is beneath it.  Thanks.
>>>>
>>>> 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: Tuesday, July 06, 2004 1:51 PM
>>>> Subject: Re: [caret-users] afni-caret link error
>>>>
>>>>
>>>>> Hi Marc,
>>>>>
>>>>> What platform are you running?  Your matrix file worked for me on
>>>>> RedHat
>>>>> 8 (with the coord file tweak, but no change to the volume name).   
>>>>> Oh
>>>>> well, if you got it working, that's all that matters.
>>>>>
>>>>> My guess on the mismatch between what caret reports and what AFNI
>>>>> reports is that AFNI is reporting on the entire volume, which  
>>>>> caret is
>>>>> reporting only the range of the metric file.  To get in the metric
>>>>> file,
>>>>> the volume had to intersect the surface, and only a subset of the
>>>>> functional volume actually intersects the surface.  So, voxels at  
>>>>> the
>>>>> upper end of the functional range were too far away from the  
>>>>> surface
>>>>> to
>>>>> be reflected in the metric file.  Note that this depends on the
>>>>> algorithm and parameters you use.  For example, if you choose  
>>>>> average
>>>>> voxel 0, only the voxel intersecting the surface will weigh in the
>>>>> metric for that node.  But if you increase the neighbors from 0 to,
>>>>> say,
>>>>> 3, then other voxels will weigh in a given node's metric value.
>>>>>
>>>>> Unlike AFNI, Caret's thresholding is based strictly on the  
>>>>> intensities
>>>>> of the functional volume you feed it.  It applies the AFNI scaling
>>>>> factor, but otherwise it isn't cognizant of the various statistical
>>>>> sub-brick types, so it doesn't modify its behavior based on that
>>>>> type. I
>>>>> wish I better understood AFNI's thresholding behavior, so I could  
>>>>> give
>>>>> you a more complete answer.  The AFNI FAQ (Q22) says, "If the
>>>>> threshold
>>>>> data brick has statistical parameters attached to it (in the .HEAD
>>>>> file), then the nominal /p/-value is shown below the threshold
>>>>> slider."
>>>>>  AFNI's threshold slider maps the range from -1 to 1, but caret's
>>>>> threshold control acts on the actual metric values (-6.866 to 2.9,  
>>>>> in
>>>>> your case).
>>>>>
>>>>> Donna
>>>>>
>>>>> On 07/06/2004 11:48 AM, Marc Malloy wrote:
>>>>>
>>>>>> Hi Donna
>>>>>>
>>>>>> I've found the problem!
>>>>>>
>>>>>> There was trailing whitespace in my .matrix file with the volume
>>>>>> name and
>>>>>> leading whitespace with the .coord file!!!!!
>>>>>>
>>>>>>
>>>>>> When I look at the values of my metric file the threshold subbrick
>>>> reports
>>>>>> fine in caret but the values reported for the view subbrick are  
>>>>>> off
>>>>>> from
>>>>>> what AFNI reports.
>>>>>>
>>>>>> afni   -6.866 to 4.12
>>>>>> caret -6.866 to 2.9
>>>>>>
>>>>>> Also about the thresholding in caret - is there anything like a p
>>>>>> value
>>>>>> (like AFNI)?  I'm not understanding what the thresholding is based
>>>>>> on in
>>>>>> caret.  Thanks.
>>>>>>
>>>>>> 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: Tuesday, July 06, 2004 11:37 AM
>>>>>> Subject: Re: [caret-users] afni-caret link error
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>> 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.5688 
>>>>>>>>>>>>> 2.c
>>>>>>>>>>>>> oord
>>>>>>>>>>>>>> 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
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>>
>>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>>> caret-users mailing list
>>>>>>>>>>>>> caret-users at pulvinar.wustl.edu
>>>>>>>>>>>>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>>>
>>>>>>>>>>>> _______________________________________________
>>>>>>>>>>>> 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
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> caret-users mailing list
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>>>>>>>>>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> caret-users mailing list
>>>>>>>>> caret-users at pulvinar.wustl.edu
>>>>>>>>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> caret-users mailing list
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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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>>>>>> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>> _______________________________________________
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>>>>>
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