[caret-users] afni-caret link error

Marc Malloy mmalloy at rotman-baycrest.on.ca
Fri Jul 9 13:46:02 CDT 2004


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.

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.56882.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
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>>>
> >>>>>>>> _______________________________________________
> >>>>>>>> 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
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>> _______________________________________________
> >>>>> 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
> >>>
> >>>
> >>>
> >>
> >>
> >> _______________________________________________
> >> 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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> caret-users at pulvinar.wustl.edu
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>





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