Re: [caret-users] Using the Caret command metric smoothing for a cortical measure saved as a text

[Harwell, John]

Files ending in MGZ appear to be FreeSurfer volume files (see 
https://surfer.nmr.mgh.harvard.edu/fswiki/FileFormats) and caret_command is 
unable to read that file format..   Try converting your files to an 
FreeSurfer’s ASCII format using the FreeSurfer program mris_convert.

While we try to support the Caret5 software, the development of Caret5 stopped 
many years ago.  You may want to consider using the Human Connectome Project’s 
“Connectome Workbench” software: 
https://www.humanconnectome.org/software/connectome-workbench

John

On Dec 3, 2017, at 10:08 PM, Rosa Shishegar 
mailto:rosita.shishe...@monash.edu>> wrote:

Dear List,

I am running into a problem trying to convert a cortical folding measurement 
saved as a text file into a Caret .metric file format. First, I convert my 
cortical folding measure to myMeasur.mgz and the surface file into 
mySyrface.mgz file format. Then I use the following line to the convert a 
FreeSurfer functional file into a Caret metric file.

caret_command -file-convert -fsf2c myMeasur.mgz mySurface.mgz myMeasur.metric

The error that I receive is "Functional data found for node with index larger 
than there are nodes in the surface.” But I double checked and it is not true.

My plan is to use the Caret metric file for the Caret command metric smoothing 
in the next step. It would be so appreciated if you could advise me how should 
I convert my surface measure to a Caret metric file. Or if I am taking the 
right steps, how can I fix the error?

Thanks,
Rosa
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Re: [caret-users] info in the deformation maps

[Harwell, John]

On Oct 20, 2017, at 4:24 PM, tony han 
mailto:oktony...@hotmail.com>> wrote:

Hi John and David,

Thanks a lot for your reply! Yes I'm thinking to move from Caret to Workbench 
since most of the time we use wb_command a lot and it makes sense to keep our 
tools up-to-date and consistent.

Just want to clarify: the weights (last 3 columns) of the vertices (indexed by 
the first 3 columns) are decided by the distance from the 3 vertices of SOURCE 
to the vertex of TARGET? If so, maybe that's the reason why why the sum of 
weights is not one for each vertex of TARGET?


While I referred to the last three columns as weights, they are actually 
triangular areas.  If you view the triangle with black and blue lines at 
http://mathworld.wolfram.com/BarycentricCoordinates.html, A1, A2, and A3 are 
the source vertices and P is the target vertex.  The last three columns in the 
file are the areas t1, t2, and t3.

So the reason why I'm looking at deformation maps is that I'm trying to figure 
out a way to quantify the deformation from native space to fs_LR at each vertex 
on the surface (32k fs_LR atlas surface). Could you give me any suggestion?

From: David Van Essen mailto:vanes...@wustl.edu>>
Sent: Friday, October 20, 2017 3:41:11 PM
To: Caret, SureFit, and SuMS software users; tony han
Subject: Re: [caret-users] info in the deformation maps

Hi Tony et al.

John’s explanation regarding deformation map files is correct.  Here, I’m 
drawing to your attention the fact that Connectome Workbench (and wb_command) 
provides improved methods for mapping from one surface mesh that has been 
registered to another (see below).  Depending on your use case scenario, you 
(and others) may decide to stick with Caret and its deformation maps (even 
though Caret is no longer under active development). Or you may find it 
advantageous to switch to wb_command for future analyses, as it has become more 
 powerful and flexible, and is still under active development 
(https://www.humanconnectome.org/software/connectome-workbench).

wb_command -label-resample
wb_command -metric-resample
   - a sphere surface with the mesh that the metric is
 currently on
   - a sphere surface that is in register with 
 and has the desired output mesh
   - the method name
The  argument must be one of the following:
  ADAP_BARY_AREA
  BARYCENTRIC
as explained in the command-line usage instructions

On Oct 20, 2017, at 2:36 PM, Harwell, John 
mailto:jharw...@wustl.edu>> wrote:

Hello,

You are correct, it is not an affine matrix.   A description of the file’s 
content is available at 
http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#deformationMapFile.

Essentially, the deformation map file defines a resampling of one surface 
triangular mesh to another.  For each vertex in the target surface, it 
identifies the corresponding location in the source surface using barycentric 
coordinates.  A barycentric coordinate contains three vertex indices that form 
a triangle and the weights define the location within the triangle.

John H

On Oct 20, 2017, at 1:00 PM, tony han 
mailto:oktony...@hotmail.com>> wrote:

Hi,

I notice that there are 6 columns of data stored in the deformation map 
(actually it's 7 but the first one looks like the indices). So what are these 
columns? It doesn't look like affine matrices? Thanks!

Best,
Tony
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Re: [caret-users] info in the deformation maps

[Harwell, John]

Hello,

You are correct, it is not an affine matrix.   A description of the file’s 
content is available at 
http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_formats.html#deformationMapFile.

Essentially, the deformation map file defines a resampling of one surface 
triangular mesh to another.  For each vertex in the target surface, it 
identifies the corresponding location in the source surface using barycentric 
coordinates.  A barycentric coordinate contains three vertex indices that form 
a triangle and the weights define the location within the triangle.

John H

On Oct 20, 2017, at 1:00 PM, tony han 
mailto:oktony...@hotmail.com>> wrote:

Hi,

I notice that there are 6 columns of data stored in the deformation map 
(actually it's 7 but the first one looks like the indices). So what are these 
columns? It doesn't look like affine matrices? Thanks!

Best,
Tony
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Re: [caret-users] strange patches on grey surface?

[Harwell, John]

On Sep 1, 2017, at 9:09 AM, Harwell, John 
mailto:john.harw...@email.wustl.edu>> wrote:

It appears that my response on Tuesday did not go through, perhaps due to a 
change in my email address.

John

Begin forwarded message:

From: "Harwell, John" 
mailto:john.harw...@email.wustl.edu>>
Subject: Re: [caret-users] strange patches on grey surface?
Date: August 29, 2017 at 9:41:22 AM CDT
To: "Caret, SureFit, and SuMS software users" 
mailto:caret-users@brainvis.wustl.edu>>

Hello,

It may be a problem with some triangles incorrectly oriented.

While viewing the left hemisphere, select these two menu items:

* Surface Menu : Topology : Orient Tiles Consistently
* Surface Menu : Normals : Generate Normals

If it fixes the problem:
* File Menu : Manage Files
* On the Manage Loaded Files Dialog, save the modified topology file.

John

On Aug 29, 2017, at 7:05 AM, Alle Meije Wink 
mailto:a.m.w...@gmail.com>> wrote:

Mapping a functional volume onto the caret surfaces made with FLIRT, I get some 
strange black/white coloured patches in only the left hemisphere.

My computer has Debian 9 (Stretch) and I have installed caret and caret-data 
from the NeuroDebian repository.
I follow the instructions of 
http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/MapVolumeToSurface:

>From main window:
 -- menu -> attributes -> map volume(s) to surface(s)
 -- data mapping type -> metric (functional) or surface shape data
 -- volume selection -> add volumes from disk ->  (thresholded to only show negative clusters)
 -- spec file and surface selection -> map to spec file -> 
Human.PALS_B12.LR.MULTI-FIDUCIAL_FLIRT_fMRI-MAPPER.B1-12.LEFT.73730.spec
spec file -> 
topology file -> Human.sphere_6.LEFT.HEM.73730.topo (no others possible)
fiducual 
coordinate files -> select all coord files (12x)
 map to spec file -> 
Human.PALS_B12.LR.MULTI-FIDUCIAL_FLIRT_fMRI-MAPPER.B1-12.RIGHT.73730.spec
spec file -> 
topology file -> Human.sphere_6.RIGHT.HEM.73730.topo (no others possible)
fiducual 
coordinate files -> select all coord files (12x)
 -- data file naming -> surface family -> 
Human.PALS_B12.LR.MULTI-FIDUCIAL_FLIRT_fMRI-MAPPER.B1-12.LEFT.73730.spec (12 
coord files)
 data file -> 
map_data_2_29_Aug_2017_12_33_32.metric
surface family -> 
Human.PALS_B12.LR.MULTI-FIDUCIAL_FLIRT_fMRI-MAPPER.B1-12.RIGHT.73730.spec (12 
coord files)
 data file -> 
map_data_3_29_Aug_2017_12_35_25.metric
 -- mapping algorithm -> metric_enclosing_voxel

Back to main window:
 -- menu -> file -> open spec file
 -- specification file: 
Human.PALS_B12.LR.MULTI-FIDUCIAL_FLIRT_fMRI-MAPPER.B1-12.LEFT.73730.spec
 coordination files -> select all
 -- metric file: map_data_0_29_Aug_2017_12_33_32.metric
 -> window captured as caret_left.png

Back to main window:
 -- menu -> file -> open spec file
 -- specification file: 
Human.PALS_B12.LR.MULTI-FIDUCIAL_FLIRT_fMRI-MAPPER.B1-12.RIGHT.73730.spec
 coordination files -> select all
 -- metric file: map_data_1_29_Aug_2017_12_35_25.metric
 -> window captured as caret_right.png

Now the right hemisphere looks brilliant (both with and without the functional 
values mapped in) but the left hemisphere has these dark to light patches all 
over the brain surface. And they appear in all models, for left, and for non in 
the right hemishere.

Is there a setting that can make the left hemispere mappings 'clean' as well?
Or should I use a different .spec file? All the examples on the internet use 
Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730.spec but I can only find 
the left and right hemispheres separately.

Many thanks for your help!

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Re: [caret-users] Caret Manual and Tutorials

[John Harwell]

You can find documentation at 
http://brainvis.wustl.edu/wiki/index.php/Caret:Documentation 
  in the sections 
Online Documentation or Tutorials.

> On Dec 15, 2015, at 1:25 PM, Rosalia Dacosta Aguayo  
> wrote:
> 
> Dear Caret team,
> 
> I have just downloaded Caret and I am highly interested in reading a Manual 
> and do some of the tutorials...what I have been not able to find themany 
> suggestion about where I can find it? and about which of your data would be 
> more suitable for doing tutorials?
> 
> Yours sincerely,
> 
> Rosalia.
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Re: [caret-users] doubt regarding fiducial mapping

[john]

> Hello Donna,
 Thank you for your response. I think now the functional and anatomical is
aligned properly once i do a reslicing(in SPM) of functional and aligning
it in par with anatomical image parameters in caret.
Thank you for your kind help,
john




Hi John,
>
> My trials with your data are detailed here:
>
>> http://brainmap.wustl.edu/pub/donna/IN/JOHN/align.html
>> login pub
>> password download
>
>
> I suspect there are better ways of dealing with oblique data, and I hope
> others will chime in if they have alternative suggestions.  (They don't
> have to be "better" -- just offering other perspectives, even.)  This was
> the best I could do with the information I have.
>
> Donna
>
>
> On Aug 20, 2015, at 12:43 PM, j...@nbrc.ac.in wrote:
>
>>> Hi Donna,
>> There were no steps that involved any de-obliquing, flipped, or
>>> shifted, AC-centered  "LPI" orientation.
>> i loaded the image, anatomical and in volume attributes I checked the
>> orientation, put the crossline at AC after shifting the image manually
>> through co ordinate values, and selected the option to keep AC position
>> as crossline position in main window. after this i gave coordinates of
>> posterior comm, and middle fissure and checked voxel size etc...
>> then i saved it as AC centered image.
>>
>>
>>
>> Hi John,
>>>
>>> Those tweaks were very helpful.  I looked at the volumes with the
>>> surface
>>> overlaid, and here's what I found:
>>>
>>> http://brainmap.wustl.edu/pub/donna/IN/JOHN/align.html
>>> login pub
>>> password download
>>>
>>> I don't trust Caret to handle oblique volumes properly.  Quoting the
>>> link
>>> above, "Can you go back through the history of this volume's processing
>>> --
>>> specifically what happened to generate anatomical_ac_centered.hdr from
>>> anatomical_image.hdr? Were there steps the de-obliqued, flipped, or
>>> shifted the anatomical to get it AC-centered and probably in "LPI"
>>> orientation, as Caret required to segment?"
>>>
>>> Donna
>>>
>>>
>>> On Aug 20, 2015, at 1:02 AM, j...@nbrc.ac.in wrote:
>>>
>>>> Hello Donna,
>>>> I've made the necessary changes and uploaded the file.
>>>>
>>>> john.
>>>>
>>>>
>>>>
>>>> If you can find your *.params file, then don't worry about the find
>>>>> command, which was intended to help you locate it if you did not know
>>>>> its
>>>>> name/location already.
>>>>>
>>>>> I looked at your dataset, and you must do two things to help me help
>>>>> you:
>>>>>
>>>>> * Remove the spaces from the filenames.  Replace them with _
>>>>> characters.
>>>>> When I try to read, move, or otherwise manipulate these files, the
>>>>> spaces
>>>>> are misinterpreted by the Linux shell as separate arguments.
>>>>>
>>>>> * Add the *.params file.
>>>>>
>>>>> After you've made those changes, rename the directory john_renamed.
>>>>> Then
>>>>> zip it and upload it.  I'll do my best to solve it.
>>>>>
>>>>>
>>>>> On Aug 19, 2015, at 1:23 AM, j...@nbrc.ac.in wrote:
>>>>>
>>>>>>> Hello Donna,
>>>>>>
>>>>>> 1.I ve tried taking the XYZ min values from .PARAMS file and
>>>>>> transformed
>>>>>> the overlay. This appears very subjective and error prone.
>>>>>>
>>>>>> 2. "Do this in your subject directory:
>>>>>>>
>>>>>>> find /my/subject/dir -name "*.params" |sort | xargs grep -i min
>>>>>> "
>>>>>>
>>>>>> I am not sure i understood this step properly
>>>>>>
>>>>>>
>>>>>> I am unable to coregister the functional image and anatomical image
>>>>>> properly.
>>>>>> I am sorry to trouble you again , but it would be great if you can
>>>>>> take
>>>>>> a
>>>>>> look at the dataset again, which i have uploaded in a folder " data
>>>>>> from
>>>>>> john.zip" at http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>>>>

Re: [caret-users] doubt regarding fiducial mapping

[john]

> Hi Donna,
There were no steps that involved any de-obliquing, flipped, or
> shifted, AC-centered  "LPI" orientation.
 i loaded the image, anatomical and in volume attributes I checked the
orientation, put the crossline at AC after shifting the image manually
through co ordinate values, and selected the option to keep AC position
as crossline position in main window. after this i gave coordinates of
posterior comm, and middle fissure and checked voxel size etc...
 then i saved it as AC centered image.







Hi John,
>
> Those tweaks were very helpful.  I looked at the volumes with the surface
> overlaid, and here's what I found:
>
> http://brainmap.wustl.edu/pub/donna/IN/JOHN/align.html
> login pub
> password download
>
> I don't trust Caret to handle oblique volumes properly.  Quoting the link
> above, "Can you go back through the history of this volume's processing --
> specifically what happened to generate anatomical_ac_centered.hdr from
> anatomical_image.hdr? Were there steps the de-obliqued, flipped, or
> shifted the anatomical to get it AC-centered and probably in "LPI"
> orientation, as Caret required to segment?"
>
> Donna
>
>
> On Aug 20, 2015, at 1:02 AM, j...@nbrc.ac.in wrote:
>
>> Hello Donna,
>> I've made the necessary changes and uploaded the file.
>>
>> john.
>>
>>
>>
>> If you can find your *.params file, then don't worry about the find
>>> command, which was intended to help you locate it if you did not know
>>> its
>>> name/location already.
>>>
>>> I looked at your dataset, and you must do two things to help me help
>>> you:
>>>
>>> * Remove the spaces from the filenames.  Replace them with _
>>> characters.
>>> When I try to read, move, or otherwise manipulate these files, the
>>> spaces
>>> are misinterpreted by the Linux shell as separate arguments.
>>>
>>> * Add the *.params file.
>>>
>>> After you've made those changes, rename the directory john_renamed.
>>> Then
>>> zip it and upload it.  I'll do my best to solve it.
>>>
>>>
>>> On Aug 19, 2015, at 1:23 AM, j...@nbrc.ac.in wrote:
>>>
>>>>> Hello Donna,
>>>>
>>>> 1.I ve tried taking the XYZ min values from .PARAMS file and
>>>> transformed
>>>> the overlay. This appears very subjective and error prone.
>>>>
>>>> 2. "Do this in your subject directory:
>>>>>
>>>>> find /my/subject/dir -name "*.params" |sort | xargs grep -i min
>>>> "
>>>>
>>>> I am not sure i understood this step properly
>>>>
>>>>
>>>> I am unable to coregister the functional image and anatomical image
>>>> properly.
>>>> I am sorry to trouble you again , but it would be great if you can
>>>> take
>>>> a
>>>> look at the dataset again, which i have uploaded in a folder " data
>>>> from
>>>> john.zip" at http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>>>>
>>>> I doubt now that there is some issue within the procedure that we
>>>> follow
>>>> in doing the analysis. So it would be best if you can check/reanalyse
>>>> the
>>>> dataset from very initial step itself.
>>>>
>>>> PS:
>>>> -anatomical image.hdr\img---unaltered structural T1 image.
>>>> -functional.hdr\imgbasic SPM8  T2*image which is to be mapped
>>>>
>>>> Thank you.
>>>>
>>>>
>>>>
>>>>
>>>> On Aug 18, 2015, at 2:19 AM, j...@nbrc.ac.in wrote:
>>>>>
>>>>>> Hello Donna,
>>>>>> Thank you for your reply.
>>>>>> Two doubts i have
>>>>>> 1. why even after loading metric as primary overlay it is not
>>>>>> getting
>>>>>> 'selectable' here in functional view (see attachment "capture")?
>>>>>
>>>>> The metric is a vertex-intensity mapping.  It is not the volume.  You
>>>>> can
>>>>> load the volume that was mapped using File: Open Data File: Volume
>>>>> Functional files.  Then it will be selectable when you map to loaded
>>>>> volume.  Or you can simply map to file on disk without loading.  But
>>>>> it
>>>>> is
>>>>> not a bad idea to load the volume, too, to make s

Re: [caret-users] doubt regarding fiducial mapping

[john]

Hello Donna,
 I've made the necessary changes and uploaded the file.

john.



 If you can find your *.params file, then don't worry about the find
> command, which was intended to help you locate it if you did not know its
> name/location already.
>
> I looked at your dataset, and you must do two things to help me help you:
>
> * Remove the spaces from the filenames.  Replace them with _ characters.
> When I try to read, move, or otherwise manipulate these files, the spaces
> are misinterpreted by the Linux shell as separate arguments.
>
> * Add the *.params file.
>
> After you've made those changes, rename the directory john_renamed.  Then
> zip it and upload it.  I'll do my best to solve it.
>
>
> On Aug 19, 2015, at 1:23 AM, j...@nbrc.ac.in wrote:
>
>>> Hello Donna,
>>
>> 1.I ve tried taking the XYZ min values from .PARAMS file and transformed
>> the overlay. This appears very subjective and error prone.
>>
>> 2. "Do this in your subject directory:
>>>
>>> find /my/subject/dir -name "*.params" |sort | xargs grep -i min
>> "
>>
>> I am not sure i understood this step properly
>>
>>
>> I am unable to coregister the functional image and anatomical image
>> properly.
>> I am sorry to trouble you again , but it would be great if you can take
>> a
>> look at the dataset again, which i have uploaded in a folder " data from
>> john.zip" at http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>>
>> I doubt now that there is some issue within the procedure that we follow
>> in doing the analysis. So it would be best if you can check/reanalyse
>> the
>> dataset from very initial step itself.
>>
>> PS:
>> -anatomical image.hdr\img---unaltered structural T1 image.
>> -functional.hdr\imgbasic SPM8  T2*image which is to be mapped
>>
>> Thank you.
>>
>>
>>
>>
>> On Aug 18, 2015, at 2:19 AM, j...@nbrc.ac.in wrote:
>>>
>>>> Hello Donna,
>>>> Thank you for your reply.
>>>> Two doubts i have
>>>> 1. why even after loading metric as primary overlay it is not getting
>>>> 'selectable' here in functional view (see attachment "capture")?
>>>
>>> The metric is a vertex-intensity mapping.  It is not the volume.  You
>>> can
>>> load the volume that was mapped using File: Open Data File: Volume
>>> Functional files.  Then it will be selectable when you map to loaded
>>> volume.  Or you can simply map to file on disk without loading.  But it
>>> is
>>> not a bad idea to load the volume, too, to make sure everything aligns
>>> properly:  Functional with surface is the important one, but the
>>> anatomical volume is the link between functional and surface (i.e., how
>>> they get aligned).
>>>
>>>> 2. what is the meaning of this error message (attachment 2), which
>>>> appears
>>>> on selecting the functional volumes?
>>>
>>> Again, the funky file naming of two of the volume files (e.g., space,
>>> parentheses, leading dashes) impedes my ability to check them quickly.
>>> But the whole brain anatomical does appear to be a NIfTI volume, rather
>>> than just an Analyze .hdr file.  I loaded it as a functional volume,
>>> and
>>> then tried to map it to your surface.  I got the same result as trying
>>> to
>>> map it from disk (clicking OK on the stickup you captured).
>>>
>>> That warning never got removed after support for nifti .hdr/.img pairs
>>> was
>>> added, but based on my getting the same results using the two paths
>>> mentioned above, I think you will solve your problem when you solve the
>>> misalignment between your cropped volume and the whole brain anatomical
>>> volume.  Alternatively, shift the surface to meet the whole brain /
>>> functional volume.
>>>
>>> Ideally, get the following loaded and aligned in caret:
>>>
>>> * whole brain anatomy volume
>>> * functional volume overlay
>>> * surface (probably shifted version of what you have now)
>>>
>>> Do this in your subject directory:
>>>
>>> find /my/subject/dir -name "*.params" |sort | xargs grep -i min
>>>
>>> Capture it to a file if it's a lot.  One of those files has the offset
>>> you
>>> need.
>>>
>>>> thank you.
>>>>
>>>>
>>>> Hi John,
>>>>>
>>>>> 

Re: [caret-users] doubt regarding fiducial mapping

[john]

> Hello Donna,

1.I ve tried taking the XYZ min values from .PARAMS file and transformed
the overlay. This appears very subjective and error prone.

2. "Do this in your subject directory:
>
> find /my/subject/dir -name "*.params" |sort | xargs grep -i min
"

I am not sure i understood this step properly


I am unable to coregister the functional image and anatomical image properly.
I am sorry to trouble you again , but it would be great if you can take a
look at the dataset again, which i have uploaded in a folder " data from
john.zip" at http://pulvinar.wustl.edu/cgi-bin/upload.cgi

I doubt now that there is some issue within the procedure that we follow
in doing the analysis. So it would be best if you can check/reanalyse the
dataset from very initial step itself.

PS:
-anatomical image.hdr\img---unaltered structural T1 image.
-functional.hdr\imgbasic SPM8  T2*image which is to be mapped

Thank you.




On Aug 18, 2015, at 2:19 AM, j...@nbrc.ac.in wrote:
>
>> Hello Donna,
>> Thank you for your reply.
>> Two doubts i have
>> 1. why even after loading metric as primary overlay it is not getting
>> 'selectable' here in functional view (see attachment "capture")?
>
> The metric is a vertex-intensity mapping.  It is not the volume.  You can
> load the volume that was mapped using File: Open Data File: Volume
> Functional files.  Then it will be selectable when you map to loaded
> volume.  Or you can simply map to file on disk without loading.  But it is
> not a bad idea to load the volume, too, to make sure everything aligns
> properly:  Functional with surface is the important one, but the
> anatomical volume is the link between functional and surface (i.e., how
> they get aligned).
>
>> 2. what is the meaning of this error message (attachment 2), which
>> appears
>> on selecting the functional volumes?
>
> Again, the funky file naming of two of the volume files (e.g., space,
> parentheses, leading dashes) impedes my ability to check them quickly.
> But the whole brain anatomical does appear to be a NIfTI volume, rather
> than just an Analyze .hdr file.  I loaded it as a functional volume, and
> then tried to map it to your surface.  I got the same result as trying to
> map it from disk (clicking OK on the stickup you captured).
>
> That warning never got removed after support for nifti .hdr/.img pairs was
> added, but based on my getting the same results using the two paths
> mentioned above, I think you will solve your problem when you solve the
> misalignment between your cropped volume and the whole brain anatomical
> volume.  Alternatively, shift the surface to meet the whole brain /
> functional volume.
>
> Ideally, get the following loaded and aligned in caret:
>
> * whole brain anatomy volume
> * functional volume overlay
> * surface (probably shifted version of what you have now)
>
> Do this in your subject directory:
>
> find /my/subject/dir -name "*.params" |sort | xargs grep -i min
>
> Capture it to a file if it's a lot.  One of those files has the offset you
> need.
>
>> thank you.
>>
>>
>> Hi John,
>>>
>>> Got your upload.  While I couldn't open the cropped volume in caret due
>>> to
>>> the way it was named, I was able to view the surface contour over the
>>> uncropped volume.  See attached capture, which shows an offset.
>>>
>>> If you have a SureFit/Caret .params file (not included in the zip), it
>>> might contain the [XYZ]min values from the cropping, which might be
>>> used
>>> to either adjust the functional volume's origin, or more likely apply
>>> an
>>> affine transform to the surface, to shift it back into alignment with
>>> the
>>> whole brain volume.  You don't have to blow away your existing coord;
>>> just
>>> rename the shifted version to indicate the offset.  This can be done
>>> via
>>> command line or using the Caret: Window: Transformation Matrix editor.
>>> The polarity of the shift (+ or -) depends on whether you're shifting
>>> the
>>> volume or surface, and I always get confused about it.  Usually I try
>>> it
>>> one way; look at the result like the capture below; and if it looks
>>> worse,
>>> I try it the other way. ;-)  One of the ways usually does the trick.
>>>
>>> Donna
>>>
>>>
>>>
>>> On Aug 12, 2015, at 9:14 AM, Donna Dierker 
>>> wrote:
>>>
>>>> Could you upload your dataset in a zip archive here:
>>>>
>>>
>>>> http://pulvinar.wustl.edu/cgi

Re: [caret-users] doubt regarding fiducial mapping

[john]

>

Ya, sorry for the incomplete query.
Our interest is to view and threshold fMRI/voxel correlation data over the
fiducial brain surface created out of high res image of individual
macaques.
1. we used CARET 5.65 for creating the fiducial surfaces(following the
caret5 tutorial guide for segmentation).we used individual already
coregistered high res images for this purpose.
2. then we tried overlaying the fMRI data(spmT file from analysis using
spm8) on the fiducial surface (following the procedures from
http://prefrontal.org/blog/2009/04/using-caret-for-fmri-visualization/
and the tutorial guides).

we ended up having
a) fiducial surfaces with fmri data mapped onto it. But the voxel
coordinates did not match properly with the results in spm8.
I should tell you one thing that we found: when we overlay whole brain
fmri results, it matches more or less in x&y axes but not in z axis. and
when we overlay results from explicitly masked analysis(roi), it seems to
be shifted caudally by 2-3mm in R-C axis. same things when checked in
spm8, shows up to be well coregistered!

b)Another issue is we are not able to threshold the caret brain overlays
in concordance with the thresholds that we use in spm.
The metric thresholding range (user defined) doesn't seems to represent
what we really need.
eg:we tried overlaying FDR corrected voel corrln values, thresh 0.4 on the
brain in caet and tried a range of metric thresholds(user scale 0-1, put
display mode-pos,thresh type -user, tried changing user pos thresh values
to 0.4 and voxels doesn't show up!

Thank you donna,





















 What software was used to reconstruct the surface?
>
> With freesurfer, there is an offset between the orig.mgz and the surface.
> And depending on many factors, you might have to flip/rotate the surface
> to be in the same orientation as the volume (or bring the volume to the
> surface).
>
> See this thread:
>
> http://www.mail-archive.com/caret-users%40brainvis.wustl.edu/msg02081.html
>
> Also see the "Check Alignment between Normalized Volume and Surface"
> section here:
>
> http://brainvis.wustl.edu/help/pals_volume_normalization/spm5_normalization_pals.html
>
> Examining the surface contour overlaid on the volum in volume view All is
> often very enlightening.
>
>
> On Aug 11, 2015, at 4:42 AM, j...@nbrc.ac.in wrote:
>
>>>
>> yes, ours is an individual s surface reconstruction, and so we checked
>> the
>> registration in spm8( using  anatomical image used for reconstruction
>> and
>> the functional image volumes used for mapping), where the volumes are
>> coregistered properly, but shows anomaly in caret.
>>
>> thank you
>>
>>
>>
>> This almost always is because the functional volume is not
>>> stereotactically registered to the anatomical volume used to generate
>>> the
>>> fiducial surface. Is this an atlas surface (e.g., one of the PALS mean
>>> midthickness surfaces), or is it an individual's surface
>>> reconstruction?
>>> If atlas, this could happen if you were trying to map SPM functional
>>> data
>>> to the AFNI mid thickness surface, for example, because there are
>>> noticeable differences between those stereotaxic spaces.
>>>
>>> If individual, make sure the functional volume is in register with the
>>> anatomical volume used to generate the surface.
>>>
>>>
>>> On Aug 10, 2015, at 1:40 AM, j...@nbrc.ac.in wrote:
>>>
>>>> Hi,
>>>>  when i map the functional data onto caret fiducial surface, it
>>>> appears
>>>> that the mapping is shifted in rostrocaudal axis, caudally, by about 2
>>>> -3 mm. anyone has idea what could be possibly wrong here?
>>>> thanks,
>>>> john
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>>>
>>>
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>>>
>>>
>>
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>
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Re: [caret-users] doubt regarding fiducial mapping

[john]

>
yes, ours is an individual s surface reconstruction, and so we checked the
registration in spm8( using  anatomical image used for reconstruction and
the functional image volumes used for mapping), where the volumes are
coregistered properly, but shows anomaly in caret.

thank you



This almost always is because the functional volume is not
> stereotactically registered to the anatomical volume used to generate the
> fiducial surface. Is this an atlas surface (e.g., one of the PALS mean
> midthickness surfaces), or is it an individual's surface reconstruction?
> If atlas, this could happen if you were trying to map SPM functional data
> to the AFNI mid thickness surface, for example, because there are
> noticeable differences between those stereotaxic spaces.
>
> If individual, make sure the functional volume is in register with the
> anatomical volume used to generate the surface.
>
>
> On Aug 10, 2015, at 1:40 AM, j...@nbrc.ac.in wrote:
>
>> Hi,
>>   when i map the functional data onto caret fiducial surface, it appears
>> that the mapping is shifted in rostrocaudal axis, caudally, by about 2
>> -3 mm. anyone has idea what could be possibly wrong here?
>> thanks,
>> john
>> ___
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>
>
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>

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[caret-users] doubt regarding fiducial mapping

[john]

Hi,
   when i map the functional data onto caret fiducial surface, it appears
that the mapping is shifted in rostrocaudal axis, caudally, by about 2
-3 mm. anyone has idea what could be possibly wrong here?
thanks,
john
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Re: [caret-users] Rendering using different colours

[John Harwell]

Hello,

Caret does have functionality that allows one to map three separate metric 
columns to a set of red, green, and blue values (rgb paint).

* Go to http://brainvis.wustl.edu/wiki/index.php/Caret:Documentation
* In the section “Tutorials”, select “PDF” next to “Caret 5.5 Tutorial - User’s 
Guide to Analysis Procedures"
* Look for the section “Viewing Three Metric (Functional) Data Sets 
Simultaneously” on page 12.


John Harwell


> On May 12, 2015, at 8:52 AM, Rocco Chiou  wrote:
> 
> Hello CARET users,
> 
> I have a question about the colour of rendering: 
> 
>  
> When rendering activation of two different tasks using different colours, I 
> need to use SPM’s imcalc to make one image negative so that they appear in 
> different colours. The negativised task would then appear blue-ish and the 
> other task would appear yellow-ish.
> 
>  
> My question now is what if I have 3 tasks… do you know if there’s a way to 
> make CARET show 3 different colour renderings on the same brain?
> 
>  
> Thanks to your answer in anticipation.
> 
>  
> Cheers,
> 
> Rocco 
> 
> 
> -- 
> Rocco Chiou, PhD
> School of Psychological Sciences, University of Manchester,
> Room T7A, Level 3, Zochonis Building, Brunswick St, Manchester M13 9PL
> Email: roccoch...@gmail.com 
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Re: [caret-users] Cutting handles?

[John Harwell]

Hi Bonnie,

The surface cuts are intended for use on a flat surface.

It is best to remove all handles in the segmentation volume prior to generating 
a surface.  There are several modes for editing segmentation voxels that 
include both adding voxels (filing the handle) and removing voxels (essentially 
cutting the handle).

* Use Volume Menu->Segmentation->Find Handles to automatically identify handles 
in the segmentation volume.
* Use Volume Menu->Segmentation->Edit Voxels  to edit segmentation voxels to 
repair handles.
* Use Volume Menu->Segmentation->Topology Report to help verify handles have 
been removed.
* Surface Menu->Topology->Correct Fiducial Surface Topology can remove handles 
from a surface.  However, there is the possibility of undesired changes to the 
surface especially when there are large handles.  

These items may be helpful:

*   http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Segmentation 
<http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Segmentation>
*   
http://brainvis.wustl.edu/wiki_linked_files/documentation/Caret_5.5_Tutorial_Segment.pdf
 
<http://brainvis.wustl.edu/wiki_linked_files/documentation/Caret_5.5_Tutorial_Segment.pdf>

John Harwell

> On Apr 29, 2015, at 1:21 AM, Bonnie Alexander  
> wrote:
> 
> 
> Hi, 
> 
> I'm wondering whether there's an option to cut handles on a surface or volume 
> rather than filling them? It appears the former is needed in some cases, but 
> I haven't seen reference to it in the documentation. I tried using 'Draw 
> Cuts' from the Surface menu, though when I use this on a .coord file it 
> doesn't draw or cut, so I suspect I'm missing something here. Any suggestions 
> on whether this is possible and how to go about it would be much appreciated. 
> 
> Also, I've been trying to locate the PALS-term12 atlas referred to in Hill et 
> al. (2010), via SumsDB, though am as yet unable to find it. If someone could 
> point me to this if it's still available, that would be great. 
> 
> Thanks,
> 
> Bonnie.
> 
>  <http://www.mcri.edu.au/>
> 
> 
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Re: [caret-users] Problem"out of memory", please help me, thank you !

[John Harwell]

When you open PALS_B12.RIGHT.DEMO.73730.spec what happens?  Do you get a dialog 
with the title "Specification File: PALS_B12.RIGHT.DEMO.73730.spec" that lists 
the names of files?  If so, (1) press the "Deselect All" button, (2) In the 
"Topology Files" group, "check" (select) all of the checkboxes, (3) In the 
Coordinate Files group, check (select) any one file and deselect all other 
files, (4), Press the Load button.

What program did you use to unzip the "PALS_B12.RIGHT.DEMO.73730.zip" file?

Have you tried to use a different computer?


John

On Jan 12, 2015, at 9:09 AM, Donna Dierker wrote:

> Scroll down to the Windows XP section:
> 
> http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/installation/caret5_installation.html
> 
> But that out of memory error still makes me wonder about the character set.  
> Unless you have a user/pc that has only an english character set that you 
> could try installing caret, I can't think of another way to test this.
> 
> 
> On Jan 10, 2015, at 5:21 AM, 陈晨  wrote:
> 
>> 
>> Thank you very much!
>> But even though I set the OS language to English, I still get an "out of 
>> memory,Caret terminating" error message when loading 
>> PALS_B12.RIGHT.DEMO.73730.spe
>> I have downloaded and  extracted caret_distribution_Windows32.v5.65.zip
>> Could you please tell me how to install Caret ?
>> 
>> Chen
>> 
>> 
>> At 2015-01-10 06:21:53,"Timothy Coalson"  wrote:
>> I think caret5 has trouble with non-english locales, if you are using a 
>> different OS language, could you try setting the OS language to english and 
>> trying it again?
>> 
>> Tim
>> 
>> 
>> On Fri, Jan 9, 2015 at 1:18 AM, 陈晨  wrote:
>> ChenChen
>> chenchen_...@163.com
>> caret5 
>> v5.65 AND Jan 27 2012 
>> Windows 7 Ultimate 
>> I get an "out of memory,Caret terminating" error message when loading 
>> PALS_B12.RIGHT.DEMO.73730.spec.
>> PALS_B12.RIGHT.DEMO.73730.zip
>> 
>> 
>> 
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>> 
>> 
>> 
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> 
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Re: [caret-users] libstdc++ version and caret5 (Timothy Coalson)

[John Harwell]

Colin,

All I can tell you is that the Red Hat system we are using for compiling is Red 
Hat Enterprise Linux Server release 5.9 (Tikanga).

John


On Feb 5, 2014, at 8:00 AM, Colin Reveley wrote:

> That's very helpful Tim/John thanks.
> 
> Can I confirm it should (at least probably) run on RHEL6 and clones (CENTOS) 
> too?
> 
> I can't test it it's for downstream colleagues. For delivering a product 
> using caret5 (and workbench).
> 
> that's very handy the RHEL5 compilation. thanks. We had the same issue a year 
> ago on CENTOS5. downgrading caret worked for whatever reason.
> 
> Colin
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Re: [caret-users] Problems after flattening - clear temp files?

[John Harwell]

Hi Tristan,

I am also using OSX 10.6.7.  Using the most recently released version of Caret, 
I was able to flatten and morph a surface without any problems.  If you are not 
using the latest version (5.64) try it to see if you still have a flattening 
problem.

Preferences, including recent spec files, are in a file name 
".caret5_preferences" in your home directory.  You can delete this file if you 
desire.

If you want, you can place your data files in a ZIP file and upload them to 
"http://pulvinar.wustl.edu/cgi-bin/upload.cgi";.  After doing so, let us know 
the name of the file and we will try flattening with your files.

John Harwell




On Jun 8, 2011, at 6:10 PM, Tristan Chaplin wrote:

> Hi,
> 
> I've been using caret for a while but just started having some trouble with 
> flattening, I'm hoping someone has a quick technical fix.  I'm using OSX 
> 10.6.7.
> 
> After running the morphing, it displays the crossover and errors screen, but 
> you can't click close, you have to force quit the process.  At this time 
> caret is using 100% cpu.  The popup also claims there are thousands of 
> crossovers, when there actually isn't any.
> 
> Sometimes a restart fixes this, but not always.
> 
> I think I've managed to get caret into a bad state and I need to clear some 
> cache or temp files.  I tried install a fresh copy of the current version but 
> it has the same problems (it still remembers all my recent spec files, I was 
> hoping it would be completely fresh).
> 
> Thanks,
> Tristan
> 
> 
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Re: [caret-users] installation problem

[John Harwell]

Missing libraries are a common problem on Linux operating systems.  You may 
have a different version of libgomp and creating a symbolic link to it may fix 
the problem.  

You will need to have root (superuser) access:

* cd /usr/lib
* ls  libgomp*

If there is any file named libgomp* (such as libgomp.so), create a symbolic 
link to it (ln -s  existing-file  missing-file) and caret should run:

* ln -s  ./libgomp.so   ./libgomp.so.1

If you do not have any "libgomp" files you will need to get a assistance from a 
system administrator or find a forum for CentOS support.

John

On May 20, 2011, at 5:18 AM, Gabriel Gonzalez Escamilla wrote:

> many thanks for you answer John,
> 
> I'd tryed to open the caret5 directly by double clicking on it and in command 
> line (adding caret to PAH) but it always says that can not open shared 
> libraries: libgomp.so.1 the  error says that the such file or directory does 
> not exist; I'm running it under CentOS 4 and and Freesusrfer v5. any ideas. 
> I've checked at my glxgears and works properly.
> 
> Gabriel
> 


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Re: [caret-users] installation problem

[John Harwell]

The "install-caret" script is no longer need.  You should be able to run caret5 
after unzipping the distribution file.

John

On May 19, 2011, at 11:11 AM, Gabriel Gonzalez Escamilla wrote:

> 
> Dear Caret users
> 
> I'm trying to instal de 64bit version of Caret, i've check that libraries are 
> ok, the thing is that when i unzip the installer and do: "chmod u+x 
> ./install-caret" it returns an error message chmod: can not accede 
> <<./install-caret>>: the file or folder does not exist, and if I actually go 
> into the caret folder there is not such file, not even before unzipping, can 
> any one help me with this?
> 
> Thanks in advanced,
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Re: [caret-users] grid of seeds

[John Harwell]

Matt,

I revised the time-series chart drawing; let me know if the drawing quality is 
satisfactory on your computer.

John

On May 3, 2011, at 8:32 AM, tony han wrote:

> Dear all,
> 
> Sorry for this beginner's question. I want to generate a 20*20 grid of 
> seeds (3mm radius spheres) on dlPFC. Then coordinates of these seeds can be 
> extracted for further analysis. How can I do these 2 steps in Caret?  Many 
> thanks!
> 
> Tony
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Re: [caret-users] QT issue + tracer metric to regional area

[John Harwell]

Effort has been underway to make the Caret source code compatible with the 
Ubuntu way of doing things.  As David mentions, we are planning to release an 
updated version of Caret very soon.  An update for Ubuntu should be available 
at the time or shortly thereafter.

I do not know what would cause the fonts to be scaled improperly.  A Google 
search for "ubuntu qt font too large" indicates the issue has occurred with 
other applications.  On other types of Linuxes, there have been buggy versions 
of the FreeType library but Caret usually crashes in this case. 

You may be able to specify a font as a parameter to caret5:
   -fn or -font font, defines the application font. The font should be 
specified using an X logical font description.  (See 
http://doc.qt.nokia.com/4.7/qapplication.html#QApplication)

John Harwell


On Feb 12, 2011, at 11:10 PM, David Van Essen wrote:

> Hi Colin,
> 
> Regarding (1), we will have a new Caret release this coming week.  I'm not 
> sure whether it's likely to help with your ubuntu problem, but Jon Schindler 
> and/or Jon Harwell might have a clue.
> 
> Regarding (2) you can use Surface: Region of Interest Operations, then select 
> all nodes; select Statistical Report in 'ROI Operation', then Create Report.  
> This will give you surface areas for all paint regions.
> 
> To get the metric-associated areas, go back to Node Selection, and choose 
> Selection Source: Metric.  Then choose the metric ROI based on threshold, and 
> generate another Statistical Report.  I think it will give you what you want, 
> including average metric value in each area.  There's also a 'Statistical 
> Paint Report' that spews out an even larger number of numbers, but probably 
> not what you want.
> 
> To get the vertex (node) set for a region, that's not something I recall 
> doing.  You might be able to do it by selecting the nodes of interest, doing 
> the Invert operation, then using the 'disconnect nodes' operation to zero 
> nodes of all but the ROI.  You could save the coord file in ASCI, then select 
> node numbers only for non-zero nodes.  
> 
> I hope this helps.
> 
> David VE
> 
> On Feb 12, 2011, at 5:07 AM, Colin Reveley wrote:
> 
>> Two questions, if you'd be kind enough:
>> 
>> 1) GUI issue
>> 
>> I've been using Caret for a while now. There is one niggle. I'm using ubuntu 
>> 10.04 64 bit. As you mentioned, the older version of caret that ships with 
>> this linux distribution has a couple of problems rendering files, and 
>> crashes sometimes.
>> 
>> So, I use the latest version from the site.
>> 
>> This works great *but* - much of the text falls off the edge of the buttons 
>> and menus. So, I have to guess what the buttons say on them. 95% this is ok, 
>> but not always.
>> 
>> I've tried changing my QT config; this does have an effect on caret but, it 
>> does not solve the issue whatever I try. QT is 4.4.1 according to caret, and 
>> that's what I have installed (and I use NVIDIA GL drivers/libraries).
>> 
>> I even tried just a full install of KDE (since that's a QT based thing) but 
>> it made no difference.
>> 
>> The funny thing is it seems fine at work, also on ubunutu 10.04. Same 
>> hardware. same software. So I've installed some package at home that's 
>> causing this issue.
>> 
>> I just can't think what it is. Although the ubuntu caret is buggy, it 
>> doesn't have these issues. I should locate it's config file and also look at 
>> what it's linking to when it runs.
>> 
>> 2) getting stats of intersection of a paint/border and a metric
>> 
>> Let us say I take a fiducial (or other representation) of F99 and I paint it 
>> only with LVE00 regions and borders. these borders and paints are very 
>> clearly defined.
>> 
>> There were two big papers LVE00; a tracer and a regional dilineation. They 
>> go together. Caret macaque standard scenes & tutorial contains much on both.
>> 
>> The nice thing is that the injection sites and results are presented as 
>> metrics on the surface.
>> 
>> So, Is there any way I can 
>> 
>> 1) get the surface area of each LVE00 region (individually). also get the 
>> vertex set for that region.
>> 2) given an injection (i.e. a metric) find out how much of the surface area 
>> of a painted region is painted also by the metric, and what intensity the 
>> metric has at each painted vertex?
>> 
>> i.e.: in each region, about how much tracer came out? I know the answer from 
>> the publications of course, but I&#

Re: [caret-users] controlling blank space in a volume montage

[John Harwell]

Michael,

You can zoom the Volume Montage just like a single slice view (Hold down CTRL 
Key while moving mouse forward).  It may partially clip the volumes.  You could 
also change the background color (File Menu->Preferences) so that it matches 
the background color in the volume slices).

John

On Jan 11, 2011, at 2:46 PM, Michael Harms wrote:

> 
> Hello,
> Is there any way to control the zoom or "blank space" between successive
> slices when displaying a Volume Montage?  Basically, I'd like to pack
> the displayed brain slices closer together...
> 
> thanks,
> -MH
> 
> 
> -- 
> Michael Harms, Ph.D.
> 
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> Renard Hospital, Room 6604   Tel: 314-747-6173
> 660 South Euclid Ave.Fax: 314-747-2182
> St. Louis, MO 63110  Email: mha...@wustl.edu
> 
> 
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Re: [caret-users] Defining ROIs/masks in CARET and exporting to volume space

[John Harwell]

If you use the Surface Region of Interest Window, set the Operation to "Create 
Volume Region of Interest".  Press the "Create Volume from Displayed Region of 
Interest Nodes".  Enter the volume size parameters in the dialog that appears 
and press the OK button.  Wait.  Save the Segmentation Volume that is created.

John



On Dec 9, 2010, at 1:41 PM, R. Matthew Hutchison wrote:

> Hi all, 
> I would like to define regions of interests/masks on the surface flat map and 
> then export them to Nifti files in the volume space.
> The goal is to use the masks for seed region analysis.
> 
> Is there a straightforward way to do this?
> 
> The "Copy current colouring to RGB volume" outputs a document file but not a 
> volume file.
> 
> 
> Thank you for your help, 
> Matt
> 
> 
> -- 
> R. Matthew Hutchison, PhD. Candidate
> Centre for Functional and Metabolic Mapping
> Robarts Research Institute
> Cuddy Wing - 9.4T Suite
> P.O. Box 5015, 100 Perth Drive
> London, Ontario, Canada  N6A 5K8
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Re: [caret-users] Freesurfer to Caret

[John Harwell]

If you want to read FreeSurfer surfaces into Caret there are several options:

* Start Caret, Select File Menu->Open Data File.  Set the File Type to "Free 
Surfer..." (there are several), select the file, and press the Open button.

* Caret's command line program "caret_command -file-convert" can be used to 
convert FreeSurface files to Caret files.

* Your version of FreeSurfer may write GIFTI (www.nitrc.org/projects/gifti) 
format files. If so, Caret is able to read GIFTI using the Open Data File 
dialog.

John

On Dec 8, 2010, at 10:40 AM, Krishna Srihasam wrote:

> Hi,
> 
> Is there any way to convert my monkey freesurfer surfaces to caret?
> 
> rgds,
> Krishna
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Re: [caret-users] Geodesic distance

[John Harwell]

Ido,

You will need to calculate geodesic distances for one of the nodes.

* Select Surface Menu->Region of Interest Operations.
* On the Surface and Topology Selection page, select your inflated surface.   
Press the Next button.
* Press the "Select Nodes" button (near bottom of dialog) to select all nodes 
(surface will turn green) and press the Next button.
* Set the Operation to Geodesic Distance.  Enter the number of a node or press 
the Choose Node With Mouse button and select the node with the mouse.  Set 
Metric and Geodesic to "Create New Column".  Press the Determine Geodesic 
Distances button.  Press the Cancel button to close the Region of Interest 
Dialog.
* On the Display Control Dialog, go to the Geodesic page and enable the 
geodesic path, if desired.
* On the Display Control Dialog, go to the Overlay/Underlay Surface page and 
set the Primary Overlay to Metric.
* Click a node and, in the Identify Window, the metric value is the geodesic 
distance.
* Save metric and geodesic distance files, if desired.

John



On Dec 8, 2010, at 9:24 AM, Ido Davidesco wrote:

> Hello,
> I`m a new user of Caret.
> I`d like to calculate the geodesic distance between 2 points on an inflated 
> surface, which was created in BrainVoyager.
> 
> I was able to load the surface in Caret. However, the Geodesic page is 
> missing in the display control dialog.
> 
> Is this option available when the surface was not created in Caret?
> 
> Thanks,
> Ido
> 
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Re: [caret-users] caret_command

[John Harwell]

Sabina,

I appears that you have the operation code in the wrong position in the command 
and each of the gray/white peaks is specified by a single value.

Try this command with using one value for the  and one value for the 
:

caret_command  -volume-segment  myanatomyfile.nii  mysegmentation.nii  
file.spec   NNYYNYYYNNYYNNN   RIGHT   
NONE   NIFTI_GZIP

John

On Dec 3, 2010, at 6:24 AM, SM Chita wrote:

> Dear CARET users,
> 
> 
> I would like to use caret to calculate the inflated, flattening, hull and in 
> the end the gyrification index for our human white matter segmentation 
> obtained using an in-house software. So I'm trying to use the "caret_command 
> -volume-segment" to generate raw and fiducial surfaces, etc. basically 
> operation-code 7 to 17. However I am not really sure what to do when i get 
> the error message:  "Too many parameters provided for operation 
> -volume-segment"
> 
> I used the following syntax: caret_command -volume-segment myanatomyfile.nii 
> mysegmentation.nii file.spec 18 20(for gray matter) 84 90(for white matter) 
> N(for no padding) RIGHT SUREFIT_THEN_GRAPH NIFTI_GZIP NY(since 
> -help says that for operation-code "all characters must be specified" )
> 
> My first question is can i use my already segmented WM to create raw and 
> fiducial surfaces , etc ? and if yes how exactly do i have to supply the 
> information for operation-code characters if i want to perform operations 
> from 7 to 17 ? 
> 
> Thank you very much for your answer !
> 
> Best regards,
> 
> Sabina  
>   
>   
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Re: [caret-users] caret5 error using large filesystem on 64-bit arch

[John Harwell]

Hi Julie,

We recently added a 64-bit version of caret5 for Linux.  From 
http://brainvis.wustl.edu/wiki/index.php/Caret:Download, download version 5.616 
(use Rabbit and Carrot to access the page).  In this version of caret, you will 
find a "bin_linux64" directory containing linux 64-bit executables.

John 

On Dec 1, 2010, at 4:07 PM, Julie Ashworth wrote:

> hi,
> I maintain computer hardware and software for the neuroscience 
> institute at UC Berkeley. Thank you for the caret software and 
> helpful support page.
> 
> We use 64-bit CentOS linux workstations, and data is stored on 
> a 24TB (XFS) filesystem mounted via NFS. 
> 
> The problem is that caret5 GUI doesn't display the contents of a 
> user's home directory. The system trace (strace) output reveals 
> the following error:
> 
> [pid 10687] statfs("/home/julie", 0xffd13f6c) = -1 EOVERFLOW (Value too large 
> for defined data type)
> 
> Apparently, caret is checking the size of the filesystem, but
> the struct (24 billion bytes / 4K blocks) is too large for the
> 32-bit statfs library.
> 
> Presumably, 64-bit binaries/libraries would resolve this problem.
> Are they available for linux?
> 
> Thanks in advance! 
> Best,
> Julie
> 
> -- 
> Julie Ashworth 
> Computational Infrastructure for Research Labs, UC Berkeley 
> http://cirl.berkeley.edu/
> PGP Key ID: 0x17F013D2
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Re: [caret-users] Controlling Foci size in Caret?

[John Harwell]

Hi John,

The "size" in spreadsheet gets placed in the focus' "extent" attribute which 
could be number of voxels or volume (millimeters cubed) of voxels in an 
activation.

On the Display Control's Foci Main Page is a "Foci Size" control.  It affects 
the size of all foci.

Each focus is mapped to a focus color and each focus color has a point size 
attribute.  Select Layers Menu->Foci->Edit Foci Colors.  Select the color used 
by a focus, adjust its Point Size, and then press the Color File Editor's Apply 
button.  Be sure to save the foci color file.

John


On Nov 16, 2010, at 1:52 PM, John Sexton wrote:

> Hello everyone, I am new to Caret and have been working my way through the 
> tutorials.
> 
> I am working with some functional connectivity data, and have successfully 
> mapped the foci into Caret.
> My next step is to scale the size of these foci based on various qualities of 
> each one.
> 
> I see that there is a field for "size" in the foci spreadsheet I filled out 
> with the coordinates and other data. 
> Will that "size" field control the size of the foci when displayed in Caret?
> 
> I looked on the example (LewisEtAl_CC00_T1.CaretFormat) and it looks like the 
> "size" field there corresponds 
> to the number of voxels at each focus, with the numbers generally in the four 
> digit range.
> 
> If I want to use some other metric, for example the relative strength of the 
> connections each one receives, 
> do those numbers need to be within a certain range or will it work with any 
> range?
> 
> Or am I wrong altogether in thinking that the Size field can control the Foci 
> size?
> 
> 
> Any help is appreciated.
> 
> Thank you,
> John
> 
> 
> 
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[caret-users] Controlling Foci size in Caret?

[John Sexton]

Hello everyone, I am new to Caret and have been working my way through the
tutorials.

I am working with some functional connectivity data, and have successfully
mapped the foci into Caret.
My next step is to scale the size of these foci based on various qualities
of each one.

I see that there is a field for "size" in the foci spreadsheet I filled out
with the coordinates and other data.
Will that "size" field control the size of the foci when displayed in Caret?

I looked on the example (LewisEtAl_CC00_T1.CaretFormat) and it looks like
the "size" field there corresponds
to the number of voxels at each focus, with the numbers generally in the
four digit range.

If I want to use some other metric, for example the relative strength of the
connections each one receives,
do those numbers need to be within a certain range or will it work with any
range?

Or am I wrong altogether in thinking that the Size field can control the
Foci size?


Any help is appreciated.

Thank you,
John
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Re: [caret-users] Flat map XYZ coodinates

[John Harwell]

Hello,

* Select File Menu->Save Data File to launch the Save Data File Dialog.
* Set the File Type to "Cell Files (*.cell).
* Set the Encoding to "Comma Separated Value File".
* At the bottom of the dialog, set Cells Associated With Surface" to the Flat 
Surface.
* Enter a name for the file.
* Press the Save button.

You should be able to load the file into a spreadsheet or text editor to get 
the coordinates.

John

On Nov 5, 2010, at 11:24 AM, Iman Janemi wrote:

> Dear Caret Users I was just wondering if there is any way I can access a text 
> file 
> 
>of the XYZ coordinates for all the cells I have in on my flat map... i 
> know these
>coordinates are stored internally because when I click on each cell on the
>map in the ID window the Cell Number Cell Name and Coordinate on flat map
>all come up along with other information ... also I know that I can access 
> a
>list of all the coordinates for the 3D model of the brain by going to the
>Cell Report section.
>Please let me know how this is possible as it would be a great help!
>Thank you!
>Iman
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Re: [caret-users] Caret in Win 7?

[John Harwell]

Problems have been reported with computers using non-English character sets 
(particularly Asian languages). The typical symptom is an out of memory 
message, often when opening a spec file. The only solution at this time is to 
use an English character set.

John



On Oct 31, 2010, at 9:11 PM, Leon Chao Liu wrote:

> Hello all,
> 
> Sorry to disturb. I have a quick question. I was trying to run Caret v5.615 
> in Windows 7 (tried both 32 and 64 version). I could open the program with no 
> problem but it halted every time when I loaded a Spec file.   Any 
> Suggestions?   
> 
> Many thanks!
> 
> -Leon
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Re: [caret-users] Custom color maps for displaying functional data

[John Harwell]

Natalia,

If you select Attributes Menu->Palette->Edit the Palette Editor will appear.  
It can be used to create and modify color palettes used for coloring functional 
data.  If you do change the palettes, be sure to save the palette file (File 
Menu->Save Data File or File Menu->Manage Loaded Files) and load it in future 
Caret sessions.

The palette file's format is the same as AFNI's palette files with some 
documentation at 
http://afni.nimh.nih.gov/pub/dist/doc/program_help/README.setup.html.

John

On Oct 12, 2010, at 6:49 PM, Natalia Bilenko wrote:

> Hi,
> 
> I was wondering if there is any way to use custom color maps to display 
> functional data in Caret, e.g. when viewing data as a metric on a flat map. 
> In particular, I have a few in-house color maps created for retinotopy data. 
> It would be great if I could use them in Caret, but I can't figure out how to 
> use anything other than the pre-loaded color maps.
> 
> Thanks for your help!
> Natalia
> 
> --
> Natalia Bilenko
> Graduate Student
> Helen Wills Neuroscience Institute
> UC Berkeley
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Re: [caret-users] strange stretched image display

[John Harwell]

Jeremy,

1) Using the Display Control's Surface Miscellaneous page, try changing Drawing 
Mode to either Nodes or Links.
2) From caret's "bin_linux" directory, try running caret5_mesa which will use 
some software OpenGL libraries included with Caret.

John



On Oct 7, 2010, at 1:59 PM, jel...@berkeley.edu wrote:

> Hello,
> 
> I seem to be getting a stretched image in the main viewing window whenever
> I load a spec file (seems to occur for any spec I try). I've attached a
> picture, but it basically looks like a triangle stretched out alopng each
> orthogonal plane.
> 
> We're running Caret on both 32-bit and 64-bit Ubuntu linux and the same
> problem is occurring on both. This problem occurred after upgrading the
> distribution on the 64-bit machine so I assume it's a driver or library
> issue. The nvidia drivers have been updated to the most recent release and
> the glxgears command runs fine. Any ideas about other settings I should
> check?
> 
> Thanks so much for your help,
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Re: [caret-users] encountering a problem of caret 5.165

[John Harwell]

Some users using non-English character sets with Windows Operating Systems have 
encountered this problem.  We have not been able to reproduce this problem and 
the only known solution is to switch to an English characters set.  

See:
* http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg01736.html
* http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg01735.html

John

On Sep 14, 2010, at 9:30 AM, Jinhui Wang wrote:

> Dear all,
> I am in Windows XP (32 bits) and encountered a problem as follows:  when i 
> launched caret 5.615, the command window showed 'MultiByteToWideChar: Cannot 
> convert multibyte text' and stopped.  What does this mean? Any helps? 
> 
> Any information is appreciated.
> 
> 
> Best
> 
> -- 
> Jin-hui Wang, Ph.D. Candidate
> Major in Cognitive Neuroscience
> State Key Laboratory of Cognitive Neuroscience and Learning,
> Beijing Normal University
> Add: No.19 Xinjiekouwai Street,
> Beijing, China. 100875
> Tel: +86 10 58802036
> Fax: +86 10 58806154
> E-mail:  wjh...@gmail.com
> wjh122...@yahoo.com.cn
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Re: [caret-users] Load *surf.gii in caret from SPM8

[John Harwell]

Hi Eugenio,

There was a bug fix for the problem you describe made on June 14th 
(http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/misc/change_log.html).  
The Caret distribution was updated yesterday so please download the latest 
Caret (http://brainvis.wustl.edu/wiki/index.php/Caret:Download) and you should 
be able to read the file.

In the event that Caret is still unable to read your GIFTI file, please upload 
the file at (http://pulvinar.wustl.edu/cgi-bin/upload.cgi) and then send me an 
email with the name of the file.

John



On Jul 22, 2010, at 9:10 AM, Abela Eugenio HCARE-KSSG-NL wrote:

> Hi John, 
> 
> thank you for the hint. However, after selecting the file, whatever surface 
> type I choose, I get an error message ("Row/Column Major order conversion 
> unavailable for arrays with dimensions greater than two").  What am I doing 
> wrong or what else do I need to know about the file before loading?
> 
> Eugenio
> 
> -Ursprüngliche Nachricht-
> Von: caret-users-boun...@brainvis.wustl.edu 
> [mailto:caret-users-boun...@brainvis.wustl.edu] Im Auftrag von John Harwell
> Gesendet: Donnerstag, 22. Juli 2010 15:37
> An: Caret, SureFit, and SuMS software users
> Betreff: Re: [caret-users] Load *surf.gii in caret from SPM8
> 
> Eugenio,
> 
> To load GIFTI files into Caret, select File Menu->Open Data File to display 
> the Open Data File Dialog.  Near the bottom of the Open Data File Dialog, set 
> the File Type to the type of GIFTI File that you would like to load.  Select 
> the GIFTI File and press the Open button to load the file.
> 
> John
> 
> On Jul 22, 2010, at 6:53 AM, Abela Eugenio HCARE-KSSG-NL wrote:
> 
>> 
>> Dear Users,
>> 
>> I'm new to caret, so this is a very basic question. I'd like to load a 
>> Gifti-File created in SPM8 into caret. How is this done?
>> 
>> Sincerely,
>> 
>> Eugenio Abela
>> Neurology St. Gallen
>> Switzerland
>> 
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> 
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Re: [caret-users] Load *surf.gii in caret from SPM8

[John Harwell]

Eugenio,

To load GIFTI files into Caret, select File Menu->Open Data File to display the 
Open Data File Dialog.  Near the bottom of the Open Data File Dialog, set the 
File Type to the type of GIFTI File that you would like to load.  Select the 
GIFTI File and press the Open button to load the file.

John

On Jul 22, 2010, at 6:53 AM, Abela Eugenio HCARE-KSSG-NL wrote:

>  
> Dear Users,
>  
> I’m new to caret, so this is a very basic question. I’d like to load a 
> Gifti-File created in SPM8 into caret. How is this done?
>  
> Sincerely,
>  
> Eugenio Abela
> Neurology St. Gallen
> Switzerland
>  
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Re: [caret-users] Adding cells to volume of standard template

[John Harwell]

Hello Matt,

There is not a way to add cells to volume slices in Caret.

You can draw borders (Layers Menu->Borders->Draw Borders) on volume slices and 
then use Layers Menu->Borders->Convert Volume Borders to Fiducial Borders.  
There is also an option Layers Menu->Borders->Convert Volume Borders to 
Fiducial Cells but there appears to be a glitch as the the cell's structure is 
not set properly.  However, if you save the Cell Projection File and then load 
it, the cells appear on the surface.

John


On Jun 16, 2010, at 11:16 AM, R. Matthew Hutchison wrote:

> Hi Caret users, 
> 
> When using the contour drawing feature, it is possible to add cells directly 
> onto the contours that can be later displayed on the reconstructed hemisphere 
> and converted to borders.
> 
> Is it possible to do this using the standard available volume? I want to be 
> able to add cells (to identify specific cortical areas) by clicking on the 
> segmentation line of the MRI image. Please see attached figure for 
> clarification. 
> 
> The goal is to then use the cells to draw the border and create paint file 
> for display.
> 
> It seems most of the options in the tutorials involve selecting areas on the 
> surface itself.
> 
> Thank you for any help or advice.
> 
> Cheers, 
> 
> R. Matt Hutchison 
> 
> 
> -- 
> R. Matthew Hutchison, PhD. Candidate
> Centre for Functional and Metabolic Mapping
> Robarts Research Institute
> Cuddy Wing - 9.4T Suite
> P.O. Box 5015, 100 Perth Drive
> London, Ontario, Canada  N6A 5K8
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Re: [caret-users] hardware acceleration under windows

[John Harwell]

Terry,

If the vendor is listed as ATI on the Help Menu->About OpenGL you appear to 
have the correct OpenGL libraries.

John

On Jun 8, 2010, at 5:58 AM, Terry Sewards wrote:

> Hi John,
> 
> I checked my OpenGL32.dll files, and they are all Microsoft versions, 
> including the one in the system32 folder. The version number is 
> 5.1.2600.2180. On the v5.61 Help Menu -> About OpenGL it says that the 
> vendor is ATI, and the OpenGL version from library is 2.0.6390. The 
> graphics do seem a little slow, especially when compared with v5.2. If I 
> get the ATI version of OpenGL32.dll, will that improve the graphics?
> 
> Terry Sewards
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> John Harwell wrote:
>> I checked the current release of Caret5 for Windows, version 5.613.  I have 
>> only one PC on which to test it, and the graphics are responsive and Direct 
>> Rendering is on (with ATI as the OpenGL vendor).
>> 
>> In the caret distribution is a directory named 
>> "lib_windows_software_opengl".  These are software OpenGL libraries and, if 
>> they are used, the graphics will be slow and Direct Rendering will be listed 
>> as Off.  These libraries should only be used when there is a problem with 
>> the computer's OpenGL libraries.  If these libraries are being used, the 
>> "OpenGL vendor" is listed as Microsoft.
>> 
>> When you view Help Menu->About OpenGL, what is listed for the "OpenGL 
>> vendor"?  It should be ATI or NVIDIA.  If the vendor is anything else, you 
>> probably are getting the wrong OpenGL libraries.  If so, search your 
>> computer for the file "OpenGL32.dll".  For any found, right click the 
>> OpenGL.dll file and select Properties from the menu.  Select the Version tab 
>> in the dialog and it will list the creator (vendor) of the library.
>> 
>> John
>> 
>> 
>> 
> 
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Re: [caret-users] hardware acceleration under windows

[John Harwell]

I checked the current release of Caret5 for Windows, version 5.613.  I have 
only one PC on which to test it, and the graphics are responsive and Direct 
Rendering is on (with ATI as the OpenGL vendor).

In the caret distribution is a directory named "lib_windows_software_opengl".  
These are software OpenGL libraries and, if they are used, the graphics will be 
slow and Direct Rendering will be listed as Off.  These libraries should only 
be used when there is a problem with the computer's OpenGL libraries.  If these 
libraries are being used, the "OpenGL vendor" is listed as Microsoft.

When you view Help Menu->About OpenGL, what is listed for the "OpenGL vendor"?  
It should be ATI or NVIDIA.  If the vendor is anything else, you probably are 
getting the wrong OpenGL libraries.  If so, search your computer for the file 
"OpenGL32.dll".  For any found, right click the OpenGL.dll file and select 
Properties from the menu.  Select the Version tab in the dialog and it will 
list the creator (vendor) of the library.

John


On Jun 6, 2010, at 7:27 AM, Raemaekers-2, M. wrote:

> Hello all,
> 
> Could it be that the latest Windows version of Caret (5.613) has a problem 
> with initiating the 3D hardware acceleration? Under the openGL menu it says 
> "OpenGL Direct Rendering: No", and the graphics are sluggish. The previous 
> version (5.6) works fine however (Direct Rendering: On and fast graphics). I 
> tested this both on a system with an NVIDIA card, and on a system with an ATI 
> card.
> 
> Kind regards,
> Mathijs Raemaekers 
> 
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Re: [caret-users] Viewing two hemispheres at the same time and changing vector colors

[John Harwell]

Hi Megan,

As Matthew mentioned in his reply, it is possible to view multiple hemispheres 
in the same window.  Each hemisphere must be in a separate spec file and when 
you load a second spec file, Caret allows one to append spec files.  When 
multiple spec files are loaded, there model selection control (below the 
toolbar) contains an "All Fiducial Surfaces" selection.  If you have both right 
and left hemispheres in the same spec file, load the spec file twice, once with 
left surfaces selected and the second time with right surfaces selected.

The vector file is in GIFTI (www.nitrc.org/projects/gifti) file format, 
although the vector file encoding has never been defined.  If you save the file 
in XML ASCII format you can load it into a text editor.  In the file are 
"DataArrays" with names Red, Green, and Blue which contain the red, green, and 
blue color components for each vector (the color component values range 0 to 
1).  If you have only a few vectors you could edit the color components.

If you are creating the vector file from an FSL volume (caret_command 
-volume-fsl-to-vector) there is an "-rgb" option that allows one to apply one 
color to all of the vectors.  

At this time, there are no options for adjusting the color components of 
vectors in Caret.

John Harwell




On May 18, 2010, at 6:42 PM, Megan Herting wrote:

> Hi,
>  
> I’m new to using Caret but I have some questions that perhaps you can help me 
> address.
>  
> First, I see in some older posts that Caret does not allow you to view both 
> hemispheres in the same window. From what I can tell this is still the case. 
> Am I correct?
>  
> Also, how can I change the Coloring Mode vector colors. For example is there 
> any way to change the XYZ as Red, Green, Blue to something else? Or if I want 
> to put vector colors in my vector file, how should those be formatted?
>  
> Thanks in advance for your help!
>  
> -Megan
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Re: [caret-users] 转发: error about the view the spec file

[John Harwell]

We have had a couple of reports of a problem similar to this on Windows 
computers that have the characters set to an Asian language instead of English. 
 I believe that switching to an English character set has resolved the problem. 
 We have not been able to reproduce the problem in our lab.

John

On Apr 27, 2010, at 6:12 AM, xuqiang_uestc wrote:

> Dear Sir
>I am a user of caret5 and I meet a problem. In linux workstation ,I can 
> easily overload the the spec files, but in windows, there comes a problem. I 
> can run the exe, and can open the menu which leads me to open the spec files. 
> But after I configure the selection, the exe  just stop and can not go on. 
> Even I leave it alone for an hour , it does not change the condition.  I have 
> tried this exe in windows xp ,windows viste and windows 7. All windows 
> operation systems failed.
> version 5.613
>  
> 2010-04-27
>  
> xuqiang_uestc
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Re: [caret-users] question about projection to surface

[John Harwell]

Paul,

You can use Layers Menu->Foci->Map Stereotaxic Foci and enter points for 
projection to the surface.  The points you entered can be saved as a foci 
projection file.  Check out 
http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Foci#Map_Stereotaxic_Foci_Dialog.
  I do not know of any way to measure spatial uncertainty.

John

On Apr 26, 2010, at 5:46 PM, Paul Aparicio wrote:

> Dear Caret Users,
> 
> I was wondering if anyone might be able to help me.  I would like to project 
> to the surface a list of arbitrary points from the volume space?  For 
> example, if I have a 3 column matrix of X, Y and Z coordinates that are 
> continuous points, not voxel indices (i.e.  [-23.4521 35.6711 62.8789 = point 
> 1; -22.6574 34.2345 63.4536 = point 2; ect..), and I would like to see where 
> these points are when projected to the reconstructed caret surface.  Also I 
> would like to know what the spatial uncertainty is in terms of the spread of 
> the projection point on the surface, is this possible?
> 
> Thanks so much for any help,
> best regards
> 
> paul
> 
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Re: [caret-users] Question about Ellipsoid parameters

[John Harwell]

Alexander,

When creating an ellipsoid from a fiducial surface, there is no way to control 
the dimensions of the resulting ellipsoid.  The operation tries to scale the 
surfaces created so that they have a surface area close to that of fiducial 
surface.

You could do the following:

* Place the ellipsoid surface in the main window.
* Select Surface Menu->Information to the get the XYZ extents of the surface.
* Determine the X, Y, and Z scaling needed to make the ellipsoid the size that 
you desire.
* Select Window Menu->Transformation Matrix Editor.
* Enter the X, Y, and Z scaling values that you calculated.
* Press the Apply Matrix to Main Window Menu.  Check the box next to Main 
Window Surface in the pop-up dialog, and press the OK button.  

Good luck.

---
John Harwell
j...@brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Apr 19, 2010, at 11:40 AM, Alex Artaki wrote:

> Hello,
> 
> I was wondering if, when inflating and converting a fiducial surface to an 
> ellipsoid, one has access to the parameters of the ellipsoid into which the 
> fiducial surface is transformed. Can one define the length, height, and width 
> of the ellipsoid? If so, where can this be done? Thank you very much.
> 
> -- 
> Alexander Artaki
> Johns Hopkins University
> Department of Biomedical Engineering - 2009
> (215) 208-1673
> 
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Re: [caret-users] caret_map_fmri

[John Harwell]

Hi Julie,

"-surface-deformation-apply" is now "-deformation-map-apply".

If you are searching for a command, try "caret_command  -help-search 
".  For example "caret_command   -help-search   deformation".

John


On Mar 29, 2010, at 10:50 AM, Julia Bender wrote:

> Hi John,
> 
> everything worked well with the script you sent me, thanks! I have another
> question: Has the caret_command "-surface-deformation-apply" also been
> replaced? I'm trying to run an older script that's calling this line, but
> I get "command not found" when I run it now. I also could'nt find it when
> I looked up all arguments under 'caret_commands -help'
> 
> thanks a lot!
> 
> Julia
> 
>> Hi Julie,
>> 
>> "caret_map_fmri" is a program that was eliminated several years ago.  Make
>> sure you have the latest version of Caret, 5.613.
>> 
>> In place of "caret_map_fmri" use "caret_command   -volume-map-to-surface".
>> 
>> Try:
>> 
>> caret_command  -volume-map-to-surface   \
>>   /mrt/Visac/01Visac/Anatomy/seg/Human.01Visac.R.Fiducial.65366.coord   \
>>   /mrt/Visac/01Visac/Anatomy/seg/Human.01Visac.R.CLOSED.65366.topo   \
>>   ""   \      <== This is the name of an input metric file to
>> which data is appended.  An empty name (two double quotes) means create
>> a new metric file.
>>   Rtest.metric   \
>>   METRIC_ENCLOSING_VOXEL  \
>>   cCue_EndoLeft.hdr
>> 
>> 
>> John Harwell
>> 
>> 
>> On Mar 26, 2010, at 9:28 AM, Julia Bender wrote:
>> 
>>> 
>>> 
>>> Hi,
>>> 
>>> I'm having trouble using caret_map_fmri. I'm running:
>>> 
>>> caret_map_fmri -m Rtest.metric -s
>>> /mrt/Visac/01Visac/Anatomy/seg/Human.01Visac.R.spec
>>> /mrt/Visac/01Visac/Anatomy/seg/Human.01Visac.R.CLOSED.65366.topo
>>> /mrt/Visac/01Visac/Anatomy/seg/Human.01Visac.R.Fiducial.65366.coord -v
>>> cCue_EndoLeft.hdr
>>> 
>>> I get:
>>> Unrecognized preferences data type
>>> BINARY:BINARY:BINARY:BINARY:BINARY:BINARY:BINARY
>>> ERROR: Error  cCue_EndoLeft.hdr: No such file or directory
>>> 
>>> I'm running the command in the directory where my statistical maps (e.g.
>>> cCue_EndoLeft.hdr) for this subject are and I have full permission on
>>> all
>>> files.
>>> 
>>> I'm using caret (current release) on a linux machine (openSUSE
>>> 11.2).Does
>>> anyone have an idea what could be wrong?
>>> 
>>> 
>>> Thanks a lot!
>>> 
>>> Julia
>>> 
>>> 
>>> 
>>> Dipl. Psych. Julia Bender
>>> Humboldt Universität zu Berlin
>>> Mathematisch - Naturwissenschaftliche Fakultät II
>>> Institut für Psychologie, Abt. Klinische Psychologie
>>> Unter den Linden 6
>>> D-10099 Berlin
>>> 
>>> 
>>> 
>>> Dipl. Psych. Julia Bender
>>> Humboldt Universität zu Berlin
>>> Mathematisch - Naturwissenschaftliche Fakultät II
>>> Institut für Psychologie, Abt. Klinische Psychologie
>>> Unter den Linden 6
>>> D-10099 Berlin
>>> 
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>>> 
>> 
>> 
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>> 
> 
> 
> Dipl. Psych. Julia Bender
> Humboldt Universität zu Berlin
> Mathematisch - Naturwissenschaftliche Fakultät II
> Institut für Psychologie, Abt. Klinische Psychologie
> Unter den Linden 6
> D-10099 Berlin
> 
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Re: [caret-users] caret_map_fmri

[John Harwell]

Hi Julie,

"caret_map_fmri" is a program that was eliminated several years ago.  Make sure 
you have the latest version of Caret, 5.613.

In place of "caret_map_fmri" use "caret_command   -volume-map-to-surface".

Try: 

caret_command  -volume-map-to-surface   \
   /mrt/Visac/01Visac/Anatomy/seg/Human.01Visac.R.Fiducial.65366.coord   \
   /mrt/Visac/01Visac/Anatomy/seg/Human.01Visac.R.CLOSED.65366.topo   \
   ""   \  <== This is the name of an input metric file to which 
data is appended.  An empty name (two double quotes) means create a new metric 
file.
   Rtest.metric   \
   METRIC_ENCLOSING_VOXEL  \
   cCue_EndoLeft.hdr
   

John Harwell


On Mar 26, 2010, at 9:28 AM, Julia Bender wrote:

> 
> 
> Hi,
> 
> I'm having trouble using caret_map_fmri. I'm running:
> 
> caret_map_fmri -m Rtest.metric -s
> /mrt/Visac/01Visac/Anatomy/seg/Human.01Visac.R.spec
> /mrt/Visac/01Visac/Anatomy/seg/Human.01Visac.R.CLOSED.65366.topo
> /mrt/Visac/01Visac/Anatomy/seg/Human.01Visac.R.Fiducial.65366.coord -v
> cCue_EndoLeft.hdr
> 
> I get:
> Unrecognized preferences data type
> BINARY:BINARY:BINARY:BINARY:BINARY:BINARY:BINARY
> ERROR: Error  cCue_EndoLeft.hdr: No such file or directory
> 
> I'm running the command in the directory where my statistical maps (e.g.
> cCue_EndoLeft.hdr) for this subject are and I have full permission on all
> files.
> 
> I'm using caret (current release) on a linux machine (openSUSE 11.2).Does
> anyone have an idea what could be wrong?
> 
> 
> Thanks a lot!
> 
> Julia
> 
> 
> 
> Dipl. Psych. Julia Bender
> Humboldt Universität zu Berlin
> Mathematisch - Naturwissenschaftliche Fakultät II
> Institut für Psychologie, Abt. Klinische Psychologie
> Unter den Linden 6
> D-10099 Berlin
> 
> 
> 
> Dipl. Psych. Julia Bender
> Humboldt Universität zu Berlin
> Mathematisch - Naturwissenschaftliche Fakultät II
> Institut für Psychologie, Abt. Klinische Psychologie
> Unter den Linden 6
> D-10099 Berlin
> 
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Re: [caret-users] simplified meshes

[John Harwell]

For some reason, after simplification, caret does not recognize the simplified 
surface as a fiducial surface.  So, save the simplified surface as fiducial 
coordinate and closed topology files, exit Caret, and restart Caret.  Restart 
the mapping process and you should be able to select Map to Caret. 

Note that the map volume to surface process maps voxel data to the surface 
nodes.  With a simplified surface you have fewer nodes and it is possible that 
an activation may fail to map to the surface where there are no nodes.


On Mar 25, 2010, at 10:13 AM, Figa Pelosa wrote:

>> If you have individual data, you could simplify the
>> individual's surface and then map the functional data to
>> it.
> 
> I'd actually need to map the fMRI data directly on the simplified mesh: If I 
> FIRST map the data on the PALS surface, and THEN simplify the mesh, I've got 
> these problems:
> 
> 1) After the mesh simplification, the colours on the mesh (the mapping of the 
> fMRI data) are gone. Furthermore, nothing happens if I change the "primary 
> overlay" settings.
> 
> 2) If I load the fMRI data again, trying a new mapping from scratch, it is 
> not possible to choose the "Map to Caret" option: I'm forced to use "Map to 
> Caret With Atlas".
> 
> 3) If I do so, and choose "metric" in the primary overlay, I've got a message 
> (in the linux shell) saying "Metric file has different number of nodes than 
> the surface." and nothing happens.
> 
> In summary, what I'd need is one of the following possibilities:
> 
> 1) To map the fMRI data on the PALS surface, then simplify the surface and 
> still be able to see, and save on file, the mapping (on the simplified 
> surface).
> 
> 2) To simplify the PALS surface and use it as an atlas (i.e., instead of the 
> PALS surface)
> 
> Thanks a lot for your help
> Ale
> 
> 
> 
> 
> 
> --- Gio 25/3/10, John Harwell  ha scritto:
> 
>> Da: John Harwell 
>> Oggetto: Re: [caret-users] simplified meshes
>> A: "Caret, SureFit, and SuMS software users" 
>> Data: Giovedì 25 marzo 2010, 13:47
>> 
>> Hello Alex,
>> 
>> Why do you need a simplified surface?  
>> 
>> If you want to map the PALS atlas you will not be able to
>> use a simplified surface.  The PALS atlas contains two
>> methods for mapping functional volumes, AFM (average
>> fiducial mapping) and MFM (multi-fiducial mapping).  We
>> recommend using MFM which maps the functional volume to 12
>> surfaces and then outputs metric data that is the average of
>> the 12 mappings.
>> 
>> If you have individual data, you could simplify the
>> individual's surface and then map the functional data to
>> it.
>> 
>> In summary, use PALS as it is.
>> 
>> John
>> 
>> 
>> 
>> On Mar 25, 2010, at 5:53 AM, Figa Pelosa wrote:
>> 
>>> hello,
>>> my name is Alex and I'm trying to map an fMRI volume
>> on a simplified version of the
>> "Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730"
>> surface.
>>> 
>>> Till now I only managed to simplify the surface, using
>> Surface->Simplify surface.
>>> 
>>> What I'd like to do is to save all the info I need
>> (e.g. files such as .metric, .coord, .topo, ...) to be able
>> to use the simplified surface as it was the original
>> suface.
>>> 
>>> Could somebody teach me how to do that?
>>> Thanks a lot
>>> Alex
>>> 
>>> 
>>> 
>>> 
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>> 
>> 
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>> 
> 
> 
> 
> 
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Re: [caret-users] simplified meshes

[John Harwell]

Hello Alex,

Why do you need a simplified surface?  

If you want to map the PALS atlas you will not be able to use a simplified 
surface.  The PALS atlas contains two methods for mapping functional volumes, 
AFM (average fiducial mapping) and MFM (multi-fiducial mapping).  We recommend 
using MFM which maps the functional volume to 12 surfaces and then outputs 
metric data that is the average of the 12 mappings.

If you have individual data, you could simplify the individual's surface and 
then map the functional data to it.

In summary, use PALS as it is.

John



On Mar 25, 2010, at 5:53 AM, Figa Pelosa wrote:

> hello,
> my name is Alex and I'm trying to map an fMRI volume on a simplified version 
> of the "Human.PALS_B12.BOTH.TEMPLATE-for-fMRI-MAPPING.73730" surface.
> 
> Till now I only managed to simplify the surface, using Surface->Simplify 
> surface.
> 
> What I'd like to do is to save all the info I need (e.g. files such as 
> .metric, .coord, .topo, ...) to be able to use the simplified surface as it 
> was the original suface.
> 
> Could somebody teach me how to do that?
> Thanks a lot
> Alex
> 
> 
> 
> 
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Re: [caret-users] Caret Logo for download?

[John Harwell]

Michael,

Those are the only images we have.  You may be able to resample it in Photoshop 
which allows one to set a physical size (inches) and dots per inch.  Gimp or 
Image Magick may offer similar options.

John



On Mar 23, 2010, at 10:34 AM, Michael Hanke wrote:

> On Tue, Mar 23, 2010 at 09:55:37AM -0500, John Harwell wrote:
>> Michael,
>> 
>> Images of the Caret logo can be found in the caret distribution's 
>> "data_files/images" directory (perhaps /usr/local/caret/data_files/images/ 
>> on your computer).
> 
> Thanks -- I saw those, but I was looking for something with higher
> resolution (this carrot has just 240 pixels height).
> 
> Thanks,
> 
> Michael
> 
> -- 
> GPG key:  1024D/3144BE0F Michael Hanke
> http://mih.voxindeserto.de
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Re: [caret-users] Caret Logo for download?

[John Harwell]

Michael,

Images of the Caret logo can be found in the caret distribution's 
"data_files/images" directory (perhaps /usr/local/caret/data_files/images/ on 
your computer).

John Harwell


On Mar 23, 2010, at 8:28 AM, Michael Hanke wrote:

> Hi,
> 
> I wonder if there is a version of the Caret logo available for download
> that has sufficient resolution to go on a poster?
> 
> Thanks in advance,
> 
> Michael
> 
> 
> -- 
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> http://mih.voxindeserto.de
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Re: [caret-users] Installing New Caret version 5.613

[John Harwell]

Jed,

I ran into numerous insurmountable problems trying to compile Caret on a Mac 
with a PowerPC processor.

There is a PowerPC version of Caret from last September that you can try.  It 
is available in "http://brainmap.wustl.edu/pub/john/"; (use the username "pub" 
and the password "download").  Get the file "caret5_exe_ppc_osx.zip" which 
contains just the caret5 application.

John


On Feb 11, 2010, at 1:50 PM, Jed Mathis wrote:

> Hi John,
> 
> That is correct mine is a powerpc. A bit outdated, thanks so much for your
> help!
> 
> Jed
> 
> 
> On 2/11/10 12:12 PM, "John Harwell"  wrote:
> 
>> Hi Jed,
>> 
>> I believe your old Mac must have a Power PC processor (from the Apply Menu,
>> select About This Mac and examine the "Processor" text).  Is it a PowerPC 
>> Mac?
>> 
>> The Mac I use is not able to build Caret executables for PowerPC Macs.
>> However, I do have access to an old Mac and should be able to build a PowerPC
>> version of Caret.
>> 
>> ---
>> John Harwell
>> j...@brainvis.wustl.edu
>> 
>> Department of Anatomy and Neurobiology
>> Washington University School of Medicine
>> 660 S. Euclid Ave   Box 8108
>> Saint Louis, MO 63110
>> 
>> 
>> 
>> 
>> On Feb 11, 2010, at 10:04 AM, Jed Mathis wrote:
>> 
>>> I attempted to download and install the new version of Caret onto my Mac
>>> (10.4.11). I unzipped the file and followed the installation instructions on
>>> the website. However when I try to run the caret.app from the macosx_apps
>>> folder I get a warning saying that the application is not supported on my
>>> system and the icon appears as attached. Any idea what I am missing?
>>> 
>>> Thanks in Advance,
>>> 
>>> Jed
>>> 
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>> 
>> 
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Re: [caret-users] Installing New Caret version 5.613

[John Harwell]

Hi Jed,

I believe your old Mac must have a Power PC processor (from the Apply Menu, 
select About This Mac and examine the "Processor" text).  Is it a PowerPC Mac?

The Mac I use is not able to build Caret executables for PowerPC Macs.  
However, I do have access to an old Mac and should be able to build a PowerPC 
version of Caret.

---
John Harwell
j...@brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Feb 11, 2010, at 10:04 AM, Jed Mathis wrote:

> I attempted to download and install the new version of Caret onto my Mac
> (10.4.11). I unzipped the file and followed the installation instructions on
> the website. However when I try to run the caret.app from the macosx_apps
> folder I get a warning saying that the application is not supported on my
> system and the icon appears as attached. Any idea what I am missing?
> 
> Thanks in Advance,
> 
> Jed
> 
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Re: [caret-users] Depth annotation volume file

[John Harwell]

Bayle,

Caret does not have the functionality you desire.

As you indicate, iterate over the voxels and find the node nearest to the 
voxel.  Note that both voxels inside and outside will have positive signs.  If 
you have a segmentation volume, you could use it to identify  voxels inside or 
outside of the surface and adjust the sign of the depth.  A more sophisticated 
method would be to find the triangle (instead of the node) nearest the voxel.

You may find these files helpful:

* caret_source/caret_brain_set/BrainModelSurfacePointLocator.cxx/h
* caret_source/caret_brain_set/BrainModelSurfacePointProjector.cxx/h

Good luck,

John Harwell


On Feb 4, 2010, at 8:19 PM, Baylis Shanks wrote:

> Hello, I'm trying to produce a functional volume file where the intensity of 
> each voxel in the brain represents the depth of that voxel from a given 
> surface. The inputs would be a volume anatomy file and a corresponding 
> surface file.
> 
> In case that is unclear, the desired function would need to iterate over each 
> voxel in the brain (according to the volume anatomy file), and, for each of 
> these, find the depth of that voxel from the surface, and record that depth 
> in the output functional volume file.
> 
> Is there already a way to do this or to almost do this in Caret? If not, I am 
> planning to extend caret_command in C++ to add this functionality.
> 
> thanks,
>   bayle
> 
> 
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Re: [caret-users] how to save cells with multiple fields of data?

[John Harwell]

Alex,

Can you include this information in the name, or class, of the cell?

John


On Jan 28, 2010, at 7:46 AM, Alex Artaki wrote:

> Hello,
> 
> I was wondering if one can create cells (and the subsequent cell files) on a 
> fiducial surface which carry multiple fields of data. In my case, each cell 
> would carry with it an x value and a y value which refer to the stimulus 
> location in visual space. What I am really hoping for is a file at the end 
> which allows me to differentiate between the cells as functions of their x 
> and y visual stimuli. Any suggestions on how to accomplish this are much 
> appreciated!!
> 
> Sincerely,
> 
> Alex Artaki
> 
> -- 
> Alexander Artaki
> Johns Hopkins University
> Department of Neuroscience
> 
> 
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Re: [caret-users] segmentation volume cut-off

[John Harwell]

Matt,

On the Segmentation Operations page, try either unchecking the Volume Error 
Correction Method or setting it to SUREFIT.  It is possible that there is a 
large topological defect and the GRAPH (based on Automated graph-based analysis 
and correction of cortical volume topology DW Shattuck, RM Leahy - IEEE Trans. 
Med. Imaging, 2001) algorithm is removing a large handle rather than filling a 
large hole (possibly the gyri that appear to touch in the left side of your 
image).

---
John Harwell
j...@brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Jan 26, 2010, at 10:31 AM, Matthew Ward wrote:

> Good morning, everyone.  I've recently encountered a problem I haven't 
> experienced before (attached).  I've segmented this brain several times 
> before (but not in a good while) with great results, but I cannot for the 
> life of me figure out why my segmentation volume is truncated about 2/3s out 
> from the midline.  I did not run a full segmentation, just a quick check on 
> the GM/WM settings (turned off 'fill ventricles', 'generate inflated/very 
> inflated/ellipsoid/cerebral hull and curvature...attributes). Any ideas on 
> why this truncation is occurring?  When setting the GM/WM cutoffs, the 
> segmentation overlay did not show this truncation.  Thanks for any help.
> 
> Best,
> 
> -- 
> Matt
>  12.png>___
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Re: [caret-users] 8857 Segmentation fault

[John Harwell]

Hi Traci,

8857 may be the ID of the process that crashed.

I just ran the volume combine command and it worked for me.

You might try "-volume-information" or "-volume-information-nifti" on each of 
the input volumes to verify that none of them are corrupt.

If you want to zip up the input volume files and upload them to 
"http://pulvinar.wustl.edu/cgi-bin/upload.cgi";, I will try to reproduce the 
error.  Let me know the name of the uploaded zip file.

John Harwell




On Jan 25, 2010, at 1:03 PM, Sandoval, Traci I wrote:

> I am trying to combine some files and I am getting the following error
> 
> 8857 Segmentation fault   
> 
> for the following command line
> 
> ${path}caret_command -volume-file-combine 
> ${analysis_path}/${sid}/${sid}_mprage/freesurfer/volume/volumes${sid}_LR.nii.gz
>  
> /home/fmridata/GW_Pilot/GW_Pilot_functional/Freesurfer_Caret_Analysis_Files/GWBR_S105/freesurfer/left/volumeGWBR_S105lh.nii.gz
>  ${analysis_path}/${sid}/${sid}_mprage/freesurfer/left/volume${sid}lh.nii.gz 
> ${analysis_path}/${sid}/${sid}_mprage/freesurfer/right/volume${sid}rh.nii.gz 
> -paint
> 
> 
> Does 8857 tell me something specific that might help me understand and 
> correct my error? Thank you, Traci
> __ 
> 
> Traci Sandoval
> Research Assistant
> NeuroPsychometric Research Lab
> School of Behavioral and Brain Sciences - University of Texas at Dallas
> Center for BrainHealth - University of Texas at Dallas
> Department of Psychiatry - University of Texas Southwestern Medical
> 
> 
> 
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Re: [caret-users] Import Freesurfer flat maps into Caret?

[John Harwell]

Hi Elise,

You can make the flat maps in Caret.  There is a tutorial for flattening 
available at http://brainvis.wustl.edu/wiki/index.php/Caret:Documentation.

Typically in the Van Essen laboratory, it is our practice to average the pial 
and smooth white matter surfaces to create a surface that approximates layer 4. 
 This can be done from the command line (caret_command -surface-average) or 
though the Caret5 GUI using File Menu->Surface Create Average Coordinate File.

Good luck,

John


On Dec 7, 2009, at 3:07 PM, Dickinson, Annelise (NIH/NIMH) [F] wrote:

> Hi Dr. Harwell,
> 
> Oh wow, that looks interesting! Hmmm I'll talk this all over with my post-doc 
> as soon as I can-but thank you so so much for all your help and advice and 
> please do let me know if you'd like any more information or data files from 
> us at all.
> 
> My post-doc's goal is to use Caret's atlases for a retinotopy experiment-do 
> you suggest simply making the flat maps themselves in Caret? If so, would you 
> happen to know the answer to the following question: Should the Fiducial 
> surface for flattening in Caret be set as the FreeSurfer smoothwm (this is 
> suggested in Beauchamp's Caret OpenWetWare flattening wiki) or another 
> FreeSurfer dataset such as pial or orig? We just want to make sure we are 
> catching all the appropriate brain tissue in the flat surface (since 
> FreeSurfer's segmetation creates different types of files from Caret's).
> 
> Please let me know if you have any insights on this issue, and thank you 
> again!!
> 
> -Elise
> 
> 
> On 12/1/09 1:59 PM, "John Harwell"  wrote:
> 
> Hello Elise,
> 
> I examined the FreeSurfer patch file and it appears to be in a different 
> format than FreeSurfer patch files we have had in the past.  While I can 
> change caret so that it does not crash, I am unable to determine the 
> organization of the file so that it can be read.  You will need to run the 
> command "mris_convert -p  lh.cort.patch.flat.try1  
> lh.cort.patch.flat.try1.asc" to convert the file to ascii format which caret 
> is able to read.  While caret is then able to read the patch file, the 
> surface from the patch file does not look correct.
> 
> John
> 
> 
> 
> *
> Annelise Dickinson
> Post-Bac IRTA
> Laboratory of Brain and Cognition, NIMH/NIH/DHHS
> Building 10, Room 4C212
> 10 CENTER DR MSC 1366
> BETHESDA  MD  20892-1366
> *
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> FAX:   (301) 402-0921
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Re: [caret-users] difficulty in flattening my partial hemisphere

[John Harwell]

Hi Alex,

We do have some instructions on manually flattening a partial hemisphere that 
may be helpful: 
http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/misc/flattening_manual.html

---
John Harwell
j...@brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Dec 6, 2009, at 11:44 AM, Alex Artaki wrote:

> Hello,
> 
> I am quite new to Caret. In short, I wish to produce a flat representation of 
> a single fold of Macaque visual cortex which includes the postlunate gyrus 
> and lunate sulcus. Cross-sections of the comprising contours are S-shaped 
> (the fiducial surface closely resembles a sheet of paper tightly curled into 
> an S). I am attaching a screen shot for further clarification. My difficulty 
> arises in the initial inflation step, where during the inflation towards a 
> sphere, the tighter curve of the S folds onto itself. I am attaching an image 
> of this as well. The geometry of my surface doesn't seem amenable to 
> flattening with the intermediate spherical method. I would love to simply 
> take both ends and stretch it out. Are there alternative ways to the 
> flattening tutorial (or is there something I've missed) to obtain a flat 
> surface from my S-shaped surface? I would appreciate any help, suggestions, 
> and direction. Thank you very much.
> 
> Alex
> 
> -- 
> Alexander Artaki
> Johns Hopkins University
> Department of Neuroscience
> Zanvyl-Kreiger Mind Brain Institute
> 
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Re: [caret-users] Import Freesurfer flat maps into Caret?

[John Harwell]

Hi Elsie,

Yes Caret5 can read FreeSurfer files.  You will need to know if the  
file is ASCII (usually ends with "asc") or binary.  You will also need  
to know if the file is a "patch" file which usually has "patch" in its  
name.  If the file is a patch file, you must open it AFTER opening a  
non-patch file such as an "orig" file.

In Caret5:
* Select File Menu->Open Data File.
* Set the File Type to "Free Surfer Ascii Surface File" or "Free  
Surfer Binary Surface File".  Select your file and press the Open  
Button.

On the command line, using caret_command (run caret_command -file- 
convert for help information):

 Convert the free surfer surface into closed topology and  
fiducial
 coordinate files.  Create a spec file for a left cortex.
 -file-convert -sc -is FSS lh.orig.asc -os CARET  
fiducial.coord \
  closed.topo FIDUCIAL CLOSED -spec file.spec - 
struct LEFT

 Convert the free surfer patch into cut topology and flat
 coordinate files.  Create or add to the spec file as left  
cortex.
 Write the coord and topo files in text format.
 -file-convert -sc -is FSP lh.oc.flat.asc lh.orig.asc \
  -os CARET flat.coord cut.topo FLAT CUT -spec  
file.spec \
  -struct LEFT -outtext




By the way, there is a committee (GIFTI, www.nitrc.org/projects/gifti)  
that has developed a common surface file format for neuroimaging file  
formats.  Both Caret and FreeSurfer are part of this committee.  In  
the not too distant future you, and others, should be able to use the  
GIFTI format for your data and move between different neuroimaging  
software applications without having to do any file format conversion.

---
John Harwell
j...@brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Nov 25, 2009, at 10:34 AM, Dickinson, Annelise (NIH/NIMH) [F] wrote:

> Hello,
>
> Sorry in advance if the answer to this question is already up  
> somewhere!
>
> I was just wondering if there is any way to import flat maps made in  
> Freesurfer into Caret for viewing and editing? If so, how would this  
> process be carried out?
>
> Please let me know, thanks so much and happy Thanksgiving!
>
> Best,
>
> Elsie
>
> *
> Annelise Dickinson
> Post-Bac IRTA
> Laboratory of Brain and Cognition, NIMH/NIH/DHHS
> Building 10, Room 4C212
> 10 CENTER DR MSC 1366
> BETHESDA  MD  20892-1366
> *
> Phone: (301) 435-4941
> FAX:   (301) 402-0921
> E-Mail : dickins...@mail.nih.gov
>
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Re: [caret-users] multiple comparison correction on SUMA data

[John Harwell]

On Nov 16, 2009, at 5:27 AM, Oers, C.A.M. van wrote:

> Hi,
>
> Although I saw a post by Donna Dierker regarding the subject, I am  
> afraid I still have a question.
>
> I have created SUMA files using a mixed model analysis. The  
> resulting files have an individual statistical threshold (and  
> coefficient). I would like to use Caret to do a multiple comparison  
> correction with a cluster size threshold.
>
> How can I convert a 1D surface file into a metric or surface_shape  
> file?
> Which way to perform the correction?
>

SUMA may be able to write its files in GIFTI (www.nitrc.org/projects/gifti 
) format which Caret is able to read and write.  Check with the AFNI/ 
SUMA team on how to convert a 1D file to GIFTI.

John

> I appreciate the help,
> Casper
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Re: [caret-users] preborder script

[John Harwell]

Alex,

Use Layers Menu->Borders->Draw Border Update.

See 
http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/dialogs/draw_border_update_dialog.html
 
.

John



On Nov 16, 2009, at 3:09 PM, Alexander Li Cohen wrote:

> Hi Donna,
> can you link to which tutorial/webpage has the description of the  
> Border Update tool? I've actually never used it
>
> -Alex
> ~)--
>
> --
> Alexander Li Cohen
> al...@npg.wustl.edu (WORK Email)
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> Medical Scientist Training Program
> Washington University in St. Louis School of Medicine
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>
> On Nov 16, 2009, at 2:11 PM, Donna Dierker wrote:
>
>> Hi ts,
>>
>> I hope you don't mind my posting your fs2caret_results.zip contents
>> here, so others can observe and/or comment:
>>
>> http://brainmap.wustl.edu/pub/donna/FREESURFER/SCRIPTS/2009_10/MSU/views.html
>> login pub
>> password download
>>
>> As you said, many are reasonable, but most need at least minor  
>> tweaking
>> to bring them into compliance with the guidelines here:
>>
>> http://brainvis.wustl.edu/help/landmarks_core6/landmarks_core6.html/
>>
>> As you mentioned, 40% of right hemispheres' calcarine landmarks  
>> extended
>> into medial wall dorsal territory (???).  One (10%) of the left hems'
>> cacarines did, also.  We haven't seen this on our end, so I'm not  
>> sure
>> what is causing it.  Could you zip up the surf directory for ONE of
>> these cases (e.g., FS003/surf); rename it to FS003.R.zip; and  
>> upload it
>> here:
>>
>> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>>
>> Now you'll get to learn how fun Caret's Layers: Borders: Border  
>> Update
>> can be to use.  Here are some specific case-by-case comments:
>>
>> FS003.L
>>   * Calcarine: trim to flush with posterior-most medial wall dorsal
>> point; it strays up into the parieto-occipital sulcus (POS) at the
>> posterior end -- pull it back into calcarine fundus (inferior  
>> branch of
>> fork).
>>   * SF_STSant (pink/magenta one):  extend a bit further inferiorly
>> near temporal pole.
>>
>> FS003.R Calcarine and Medial Wall: should terminate just posterior  
>> and
>> inferior to the splenium, which is just inferior to where the medial
>> wall dorsal (MWD) should terminate and the medial wall ventral (MWV)
>> should start.  Because it looks like the MWV is extending into dorsal
>> territory, you'll need to erase the roguy dorsal segment, and  
>> extend the
>> MWD from the posterior end.  Look at the other cases and the core 6
>> landmarks page as a guide.
>>
>> FS006.L Calcarine posterior end strays up into POS -- pull it back  
>> into
>> calcarine fundus (inferior branch of fork).
>>
>> FS006.R See comments on FS003.R Calcarine and Medial Wall.
>>
>> FS007.L The MWD misses some non-cortical area near genu -- tweak it.
>>
>> FS007.R The sylvian anterior goes rogue, needs trimming.
>>
>> FS008 -- thank this subject for having representative anatomy (no  
>> left
>> or right complaints).
>>
>> FS009.R See comments on FS003.R Calcarine and Medial Wall.
>>
>> FS010.L The sylvian anterior goes rogue, needs trimming.
>>
>> FS012.L It is unlikely (but possible) that a bad talairach.xfm caused
>> border drawing to fail altogether.  Perhaps it was something more
>> mundane, like one o

Re: [caret-users] cluster level size, ICBM53 brain template, mapping focus in a volume

[John Harwell]

On Nov 13, 2009, at 4:09 PM, spou...@mclean.harvard.edu wrote:

> Dear Caret users,
>
> I have 3 questions:
>
> 1-I am mapping stereotaxic foci from structural studies. These studies
> report peak but also cluster level size. Is there any way to code that
> information?

If none of the fields on the Map Stereotaxic Foci dialog seem  
appropriate, use the comment field.

>
> 2-I am trying to map a study done using the ICBM53 average brain  
> template.
> This is not in the options for mapping stereotaxic focus. Anyone has a
> suggestion about the one to select?
>
> 3-Is there any way to map a stereotaxic focus in a volume and not  
> only on
> surface?
>

Yes.

1) If the foci have not been projected, project them using Layers Menu- 
 >Foci->Project Fiducial Foci or Layers Menu->Foci->Project Foci to  
PALS Atlas.
2) Select Layers Menu->Foci->Unproject Foci to Volume.  It is best  
that the surface(s) chosen, are in the same stereotaxic space as the  
volume on which the foci will be viewed.
3) On the Display Control's Foci Main Page, check the Show Volume Foci  
checkbox.
4) If desired, save the foci projection file so that foci volume  
coordinates are available next time.

John

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Re: [caret-users] Beginner's question about right location of PALS atlas

[John Harwell]

Stephane,

When projecting foci to the PALS atlas, Caret is looking for files in  
the directory "data_files/fmri_mapping_files" within the caret  
installation directory.  For you, it appears that this should be / 
Applications/caret/data_files/fmri_mapping_files".  Do you have this  
directory and is there anything in it?  Which version of Caret are you  
running (listed in the main window titlebar)?

John


On Nov 8, 2009, at 9:06 PM, spou...@mclean.harvard.edu wrote:

> Dear Caret users,
>
> I am a newcomer in the world of Caret and I am going over the  
> tutorial. I
> have a small problem with one of the proposed examples.
>
> In the Caret Tutorial - the Basics of Sept 22nd 2006, page 28 point  
> 1.23.2
> Projecting Foci: when I perform this step, a get a popup saying  
> "Unable to
> find PALS atlases.  Is caret installed properly?"
>
> My computer is a Mac and the OS is Leopard.
> I use the latest version of Caret.
> I installed the folder CARET_TUTORIAL_SEPT06 that contains the PALS
> atlases in /Applications/caret/caret5_help/tutorials
>
> What am I missing?
>
> Thanks for you help
>
> Stephane
>
>
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>

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Re: [caret-users] installation

[John Harwell]

Joost,

Caret is compiled on a 32-bit Linux operating system and you  
apparently have a 64-bit Linux operating system.  You should be able  
to install the 32-bit runtime libraries on your computer  (check with  
the vendor of your Linux distribution) and then Caret should run.  We  
had this problem with a recently purchased computer from Dell with Red  
Hat Linux.

---
John Harwell
j...@brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Nov 2, 2009, at 10:39 AM, j janssen wrote:

> Hi,
>
> downloaded: caret_distribution.v5.612.zip
> my system: Linux neuro2 2.6.27.24-170.2.68.fc10.x86_64 #1 SMP Wed  
> May 20 22:47:23 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
> error message after installation: ./caret5: error while loading  
> shared libraries: libpng12.so.0: wrong ELF class: ELFCLASS64
>
> FYI:
> [ne...@neuro2 bin_linux]$ ldd caret5
> linux-gate.so.1 =>  (0x00828000)
> libpng12.so.0 => not found
> libSM.so.6 => not found
> libICE.so.6 => not found
> libXi.so.6 => not found
> libXrender.so.1 => not found
> libXrandr.so.2 => not found
> libfreetype.so.6 => not found
> libfontconfig.so.1 => not found
> libXext.so.6 => /usr/lib/libXext.so.6 (0x0095e000)
> libX11.so.6 => /usr/lib/libX11.so.6 (0x0011)
> libz.so.1 => /lib/libz.so.1 (0x00ada000)
> libgthread-2.0.so.0 => not found
> libglib-2.0.so.0 => not found
> librt.so.1 => /lib/librt.so.1 (0x00724000)
> libpthread.so.0 => /lib/libpthread.so.0 (0x00d14000)
> libdl.so.2 => /lib/libdl.so.2 (0x00549000)
> libGLU.so.1 => not found
> libGL.so.1 => not found
> libm.so.6 => /lib/libm.so.6 (0x00378000)
> libc.so.6 => /lib/libc.so.6 (0x003a1000)
> libXau.so.6 => /usr/lib/libXau.so.6 (0x0057b000)
> libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0x00525000)
> libxcb.so.1 => /usr/lib/libxcb.so.1 (0x00de1000)
> /lib/ld-linux.so.2 (0x00216000)
> libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x0067d000)
>
> any thoughts?
>
> thanks,
> -joost
>
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Re: [caret-users] countour cell question

[John Harwell]

Hello Lindsey,

The code that performs unprojection of a cell is listed below.   
Closest tile vertices are the three nodes that define a triangle.   
Closest tile areas are used to define a barycentric coordinate 
(http://en.wikipedia.org/wiki/Barycentric_coordinates_(mathematics) 
) within the triangle.  As the triangle changes in shape, the  
barycentric coordinate maintains the same position relative to the  
nodes that form the triangle.

"cdistance" was used in the past, but it was not placing the cell in  
the correct location.  It was replaced by "signedDistanceAboveSurface"  
which is the distance, parallel to the direction of the tile's normal  
vector, of the cell from the barycentric coordinate within the  
triangle.  "signedDistanceAboveSurface" is positive when the cell is  
above the surface and negative when then the cell is under the surface.

If you just want to know the distance of the cell from the surface,  
look at "signedDistanceAboveSurface".

John



/**
  * Unproject an inside triangle projection.
  */
bool
CellProjection::unprojectInsideTriangle(const CoordinateFile& cf,
 const TopologyFile& tf,
 const bool  
pasteOntoSurfaceFlag,
 float xyzOut[3]) const
{
const float* v1 = cf.getCoordinate(closestTileVertices[0]);
const float* v2 = cf.getCoordinate(closestTileVertices[1]);
const float* v3 = cf.getCoordinate(closestTileVertices[2]);

const TopologyHelper* th = tf.getTopologyHelper(false, true, false);
if ((th->getNodeHasNeighbors(closestTileVertices[0]) == false) ||
(th->getNodeHasNeighbors(closestTileVertices[1]) == false) ||
(th->getNodeHasNeighbors(closestTileVertices[2]) == false)) {
   return false;
}

float t1[3], t2[3], t3[3];
for (int i = 0; i < 3; i++) {
   t1[i] = closestTileAreas[0] * v3[i];
   t2[i] = closestTileAreas[1] * v1[i];
   t3[i] = closestTileAreas[2] * v2[i];
}

const float area = closestTileAreas[0] + closestTileAreas[1]
 + closestTileAreas[2];

float projection[3] = { 0.0, 0.0, 0.0 };
if (area != 0) {
   for (int i = 0; i < 3; i++) {
  projection[i] = (t1[i] + t2[i] + t3[i]) / area;
   }
}
//
// Note: that does caret4 style clockwise orientation
//
float tileNormal[3];
MathUtilities::computeNormal((float*)v3, (float*)v2, (float*)v1,  
tileNormal);

for (int j = 0; j < 3; j++) {
   if (pasteOntoSurfaceFlag) {
  xyzOut[j] = projection[j];
   }
   else if (signedDistanceAboveSurface != 0.0) {
  xyzOut[j] = projection[j] + tileNormal[j] *  
signedDistanceAboveSurface;
   }
   else {
  xyzOut[j] = projection[j] + cdistance[j];
   }
}

return true;
}



On Sep 29, 2009, at 7:50 PM, Lindsey Leigland wrote:

> Hello,
>
> I am trying to determine the distance between a contour cell and the  
> fiducial surface I created from a number of contours.  (I have  
> marked an area within one of my 2D contours and am trying to  
> determine the area’s coordinates in terms of the 3D surface and/or  
> the distance from the 3D surface).
>
> In the cell projection file, a field called “cdistance” is followed  
> by 3 numbers, but I wasn’t sure what these numbers represent, or if  
> they could help me determine the distance from the surface to my  
> contour cell.  I also wasn’t sure what the numbers were following  
> the “closest tile vertices” or “closest tile areas” fields.
>
> If anyone had any information that could help, I would greatly  
> appreciate it.
>
> Thank you,
> Lindsey
>
> Lindsey Leigland
> Departments of Behavioral Neuroscience and the Advanced Imaging  
> Research Center
> Oregon Health & Science University L452
> 3181 SW Sam Jackson Park Road
> Portland, OR 97220
> Phone: 503-418-8835
> Fax: 503-418-1543
>
> ___
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> http://brainvis.wustl.edu/mailman/listinfo/caret-users


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Re: [caret-users] [Fwd: question]

[John Harwell]

Hello,

I used the data set you listed and I was able to project foci on a Mac  
without any errors.

However, if caret is not installed properly, it is possible that foci  
projection to the PALS atlas will crash.  Do you get a message that  
pops up when caret is started indicating that caret is not installed  
properly?

The 5.611 development version downloadable from 
"http://brainvis.wustl.edu/wiki/index.php/Caret:Download 
" has been updated.

John

On Aug 31, 2009, at 11:05 AM, spou...@mclean.harvard.edu wrote:

>  Original Message  
> 
> Subject: question
> From:spou...@mclean.harvard.edu
> Date:Mon, August 31, 2009 12:03 pm
> To:  caret-users@brainvis.wustl.edu
> --
>
> YOUR NAME: Stephane Poulin
>
> YOUR EMAIL ADDRESS: spou...@mclean.harvard.edu
>
> NAME OF PROGRAM (caret5 or caret_command): caret5
>
> VERSION AND DATE (at top of main window in caret5 or run caret_command
> without any parameters): caret v5.61 (August 2009)
>
> OPERATING SYSTEM (Mac/Windows/Linux) AND VERSION (Mac: Apple Menu- 
> >About
> this Mac) (Linux: Run "uname -a" in a terminal window) (Windows: Start
> Menu->Control Panel->System or Start Menu->Control Panel- 
> >Performance and
> Maintenance->System): Mac version 10.5.7
>
> SUMMARY OF PROBLEM:
> Doing the tutorial (Caret_Tutorial_Oct06.pdf), completing step 1.23.2
> "Projecting foci
> • Select Layers: Foci: Project Foci to PALS atlas
> • Press OK on the Foci Projection Map to PALS Atlas popup."
>
> When I press ok on the Foci Projection Map to PALS Atlas popup I  
> receive
> the following message:
>
> "Caret will be terminating due to an unexpected exception.
> abort() will be called and a core file may be created."
>
> HOW TO REPRODUCE PROBLEM:
> The problem happens whenever I tried it.
>
> WHAT SHOULD HAPPEN:
> If the step was working properly, all of the loaded foci should be
> projected to the atlas surface and would progressively become  
> visible in
> the other windows (inflated and flat surfaces).
>
> NAME OF UPLOADED DATA ZIP FILE: tutorial data set  
> (CARET_TUTORIAL_SEPT06)
> file PALS_B12.RIGHT.DEMO.73730.spec
>
>
> Thanks very much for your help
>
> Stephane Poulin
>
>
> ___
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> caret-users@brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users
>


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Re: [caret-users] can we change the minimum value of the colorbar?

[John Harwell]

Yune,

You can use the User Scale on the Display Control's Metric Settings  
Page 
(http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/dialogs/display_control_dialog.html#MetricSelectionPage
 
) to control the mapping of metric values into a color palette.  Set  
"Pos Min" to 4 and "Pos Max" to the maximum positive value in the  
metric data.  To get the maximum positive metric value, go to the  
Display Control's Metric Selection page and press the "H" button in  
the row that is selected as the "View" column.

John


On Jul 31, 2009, at 2:15 PM, Yune S. Lee wrote:

>
> Hello Caret users,
> Is there any way to change the minimum value of the color bar as we
> define in the user threshold type?
> For instance, I found out that even if I set the user threshold to 4,
> the minimum value of the color bar still begins with 0.
> I can clearly see that the dark orange (when palatte was chosen PSYCH)
> now shows the areas whose t value is higher than 4, not 0 under the  
> new
> threshold, but the minimum value of the
> colorbar does not match with the degree of color.
> Any help would be greatly appreciated.
>
> Thanks,
> YSL
>
>
>
>
>
>
>
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>

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Re: [caret-users] A strange display for the CARET interface

[John Harwell]

Liang,

Most likely, the problem is with the computer's graphics card drivers  
and OpenGL libraries.  You will need to install the latest graphics  
drivers and you can get them from the manufacturer of the graphics  
card.  This is a very common problem on Linux.

In the meantime, you can try running "caret5_mesa".  This command uses  
a software version of the OpenGL libraries but operations will be  
slow.  If the surface appears correctly using "caret5_mesa" the  
problem is definitely with the graphics card drivers.

John Harwell



On Jul 23, 2009, at 8:16 PM, liang wang wrote:

> Hi CARET experts,
>
> Under Windows opposition system, CARET works well for me. Currently,  
> I install it on Linux platform (RedHat, 64bit). How, a strange  
> attached picture with a little part of brain shows up on the screen  
> when loading a spec file. Does anyone give some advice to solve it. .
>
> Thanks
>
> Liang
> -- 
> Liang Wang, PhD
> Postdoctoral Fellow
> Woodward Lab
> Department of Psychiatry
> University of British Columbia
> BC Mental Health & Addiction Services
> 938 West 28th Avenue
> Vancouver BC V5Z 4H4
> Telephone: 1-604-875-2000 (ext. 4735)
> Fax: 1-604-875-3871
> Email: wangl...@gmail.com
> ___
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Re: [caret-users] 64bit Linux and performance of Error Correction while Segmenting

[John Harwell]

Marek,

It is not unusual for a segmentation's error correction staget to take  
one hour.  The time required by error correction depends upon the  
quality of the initial segmentation; the more errors, the longer error  
correction requires.

Twenty hours is much longer that I would expect.  caret5_mesa should  
only be used to help determine if there are problems with the linux  
computer's Open GL libraries and graphics card drivers.

If the surfaces generated are of good quality you are using caret  
correctly.  If the gray/white peaks were incorrect or if removal of  
non-cortical structures failed, that could cause excessive error  
correction.

Very little of caret is multi-threaded so using 100% of one core is  
typical.

John Harwell


On Jul 21, 2009, at 4:59 AM, eep...@bangor.ac.uk wrote:

> Hi,
>
> I am experiencing some long waiting times while running segmentation
> on a pre-packaged Caret 5.61. Today it amounted to 1 h (when ran
> caret5), the other day to 20 h (when ran caret5_mesa). It is
> especially the Auto Error Correction stage that takes long to compute.
> Apparently, the same dataset on a Mac takes approx. 20-30 min to be
> processed.
>
> The machine is x86_64 GNU/Linux Ubuntu running 2.6.28-14-generic
> #46-Ubuntu SMP kernel. CPU is Intel Xeon X5355 (quad core, @2.66 GHz
> each, ca. 5300 BogoMIPS each; model 15, stepping 7). 4 GB RAM, 12 GB
> swap.
>
> top reveals that caret5 is grinding only one of the cores (@100%),
> however, I am given to understand that this is only to be expected
> ("User's Manual and Tutorial").
>
> As I was only introduced to Caret a few days ago, my first suspicion
> is that I have been making some silly mistakes. Are there any obvious
> and not-so-obvious things to check that would explain such long
> computation time?
>
>
> With kind regards,
> Marek Ludwikow
>
> 
> This message was sent using IMP, the Internet Messaging Program.
>
>
> -- 
> Gall y neges e-bost hon, ac unrhyw atodiadau a anfonwyd gyda hi,
> gynnwys deunydd cyfrinachol ac wedi eu bwriadu i'w defnyddio'n unig
> gan y sawl y cawsant eu cyfeirio ato (atynt). Os ydych wedi derbyn y
> neges e-bost hon trwy gamgymeriad, rhowch wybod i'r anfonwr ar
> unwaith a dilëwch y neges. Os na fwriadwyd anfon y neges atoch chi,
> rhaid i chi beidio â defnyddio, cadw neu ddatgelu unrhyw wybodaeth a
> gynhwysir ynddi. Mae unrhyw farn neu safbwynt yn eiddo i'r sawl a'i
> hanfonodd yn unig  ac nid yw o anghenraid yn cynrychioli barn
> Prifysgol Bangor. Nid yw Prifysgol Bangor yn gwarantu
> bod y neges e-bost hon neu unrhyw atodiadau yn rhydd rhag firysau neu
> 100% yn ddiogel. Oni bai fod hyn wedi ei ddatgan yn uniongyrchol yn
> nhestun yr e-bost, nid bwriad y neges e-bost hon yw ffurfio contract
> rhwymol - mae rhestr o lofnodwyr awdurdodedig ar gael o Swyddfa
> Cyllid Prifysgol Bangor.  www.bangor.ac.uk
>
> This email and any attachments may contain confidential material and
> is solely for the use of the intended recipient(s).  If you have
> received this email in error, please notify the sender immediately
> and delete this email.  If you are not the intended recipient(s), you
> must not use, retain or disclose any information contained in this
> email.  Any views or opinions are solely those of the sender and do
> not necessarily represent those of the Bangor University.
> Bangor University does not guarantee that this email or
> any attachments are free from viruses or 100% secure.  Unless
> expressly stated in the body of the text of the email, this email is
> not intended to form a binding contract - a list of authorised
> signatories is available from the Bangor University Finance
> Office.  www.bangor.ac.uk
>
>
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Re: [caret-users] t-test iteration quits

[John Harwell]

Akiko,

We do limit the number of iterations to "2 to the Nth power" where N  
is the number of columns in the input metric file.  If you are being  
limited to 16 iterations, it implies that your metric file contains 4  
columns.  To create the randomized file for the one-sample T-Test,  
each column of data is multiplied by a positive or negative one.
Since each column has two possible values, "2 to the N" is the maximum  
number of unique permutations.  See pages 18-20 of Nonparametric  
Permutation Tests for Functional Neuroimaging: A Primer with Examples  
by Thomas E. Nichols and Andrew P. Holmes in Human Brain Mapping  
15:1-25 (2001).

However, if you have more than four columns in your metric file, try  
the latest version of Caret, 5.611, available from 
http://brainvis.wustl.edu/wiki/index.php/Caret:Download 
.  Note that the command "-metric-or-shape-stat-one-sample-t-test" has  
been renamed to "-metric-statistics-one-sample-t-test".  If the  
problem still occurs, please let us know.

---
John Harwell
j...@brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Jul 16, 2009, at 6:04 PM, Akiko Ikkai wrote:

> Hi,
>
> I'm trying to run one-sample t-test from the command line, and  
> having this strange problem of iteration quitting at 16th  
> permutation, or fewer. If I give iteration fewer than 16, it runs  
> fine, but anything above it, it quits at 16. I can't seem to find  
> where this magic number 16 is coming from. Below is the command I'm  
> running:
>
> for EACHMETRIC in `ls *LH*.metric`;
> do
> /usr/local/caret-5.51/bin/caret_command -metric-or-shape-stat-one- 
> sample-t-test ${EACHMETRIC} /hyper/library/caret_files/ 
> Human.PALS_B12.LEFT_AVG_B1-12.FIDUCIAL_711-2C.clean.align. 
> 73730.coord /hyper/library/caret_files/Human.sphere_6.LEFT_HEM. 
> 73730.topo /hyper/library/caret_files/ 
> deformed.Human.LH.Group.surface_shape 3 T-Map_${EACHMETRIC}  
> Permuted_T-Map_${EACHMETRIC} `basename ${EACHMETRIC} .metric`.paint  
> T-Stats_`basename ${EACHMETRIC} .metric`.metric T-Stats_`basename $ 
> {EACHMETRIC} .metric`.txt -2.5 2.5 0.1 10 1 100 0 4 ;
> done
>
> we are running caret version 5.51 on Mac.
> ... any insights?
>
> Thanks in advance! Akiko
>
> Akiko Ikkai
> PhD Candidate
> Department of Psychology
> New York University
> 6 Washington Place
> New York NY, 10003
>
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Re: [caret-users] Caret GUI menu items were truncated (linux pre-built version)

[John Harwell]

Hiko,

You can try the development version of caret, 5.611, from 
http://brainvis.wustl.edu/wiki/index.php/Caret:Download 
.  It uses QT 4.4.1.

My only other suggestion, to you and others, is do not use Linux.  You  
might visit the pro-Linux website, http://www.whylinuxsucks.org/.

John Harwell



On Jul 8, 2009, at 12:37 PM, HIKO Y. Yu wrote:

>
> Are you using a non-English character set on your computer?  If so,
> try switching to the English character set and see if that helps.
>
> Run "caret5 -help".  There is a "-style" option.  Try starting caret5
> with each of the styles to see if one of them helps.
>
> Linux user of Caret have had problems with the FreeType library (which
> is used for rending text by QT) in the past.  Is your computer up to
> date with patches?
>
> John
>
>
> Dear John and lists
>
> I am actually using English character set as default.
> This is what my `locale` looks like:
> LANG=en_US.UTF-8
> LC_CTYPE="en_US.UTF-8"
> LC_NUMERIC="en_US.UTF-8"
> LC_TIME="en_US.UTF-8"
> LC_COLLATE="en_US.UTF-8"
> LC_MONETARY="en_US.UTF-8"
> LC_MESSAGES="en_US.UTF-8"
> LC_PAPER="en_US.UTF-8"
> LC_NAME="en_US.UTF-8"
> LC_ADDRESS="en_US.UTF-8"
> LC_TELEPHONE="en_US.UTF-8"
> LC_MEASUREMENT="en_US.UTF-8"
> LC_IDENTIFICATION="en_US.UTF-8"
> LC_ALL=
> The "-style" option doesn't make things better either.
> The version to my freetype package is  
> "freetype-1.3.1-1392.4" (OpenSUSE 11.1).
> It's the latest version I can get.
> Interestingly, I noticed that Caret5 is using Qt 4.1 and seems to be  
> static-linked.
> My system use Qt 4.5.1 which does not exhibit truncation of texts as  
> those in Caret.
> It seems unlikely to make Qt dynamically linked in Caret unless I  
> rebuild it, but I made efforts on it and there's lots of technical  
> difficulties such as undefined symbols like "vtkPatented"...
>
> Hiko
>
>
> >
> > Message: 3
> > Date: Fri, 26 Jun 2009 21:16:50 -0500 (CDT)
> > From: Donna Dierker 
> > Subject: Re: [caret-users] Caret GUI menu items were truncated  
> (linux
> >pre-built version)
> > To: "Caret, SureFit, and SuMS software users"
> >
> > Message-ID:
> ><50425.68.94.88.238.1246069010.squir...@brainvis.wustl.edu>
> > Content-Type: text/plain;charset=iso-8859-1
> >
> > Enter "caret5 -help" at the command line.  There is an option like
> > --Cleanlooks or something like that that makes me happy with Caret
> > on my
> > Linux desktop.  Give it a shot.
> >
> > If it makes you happy, too, consider aliasing "caret" to "caret5
> > --Cleanlooks" (or whatever the option actually is).  I'm not at a
> > computer
> > that has Caret installed.  Shocking, I know.
> > Thanks a lot for the information
> >
> > I gave it a try on the command-line option
> > That did a great improvement on the layout style but the problem is
> > still there
> > Maybe a picture can make my point more straightforward:
> > http://img151.imageshack.us/img151/6825/rect3170.png
> > Red dotted-boxes show where those truncated items are.
> > Apparently, changing GUI style cannot alleviate the problem.
> >
> >
> > > Dear Caret experts
> > >
> > > I tried Caret versions of 5.61 and 5.611 on my linux PC (OpenSUSE
> > 11.1
> > > 64-bit edition).
> > > They got the same problem that makes items on menubar truncated.
> > > For example, the 3rd item under the "Surface" menu now looks like
> > "Convert
> > > Main Window Surface to Segmenta".
> > > Even though Caret GUI layout is controlled by Qt but there is no
> > way to
> > > change its layout style with qtconfig.
> > > This is quite annoying and prevents me from knowing what a  
> button's
> > > function
> > > is by reading the text on it.
> > >
> > > Does anyone know how to fix it?
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Re: [caret-users] caret-users Digest, Vol 69, Issue 14

[John Harwell]

Are you using a non-English character set on your computer?  If so,  
try switching to the English character set and see if that helps.

Run "caret5 -help".  There is a "-style" option.  Try starting caret5  
with each of the styles to see if one of them helps.

Linux user of Caret have had problems with the FreeType library (which  
is used for rending text by QT) in the past.  Is your computer up to  
date with patches?

John

On Jun 27, 2009, at 3:57 PM, HIKO Y. Yu wrote:

>
> Message: 3
> Date: Fri, 26 Jun 2009 21:16:50 -0500 (CDT)
> From: Donna Dierker 
> Subject: Re: [caret-users] Caret GUI menu items were truncated (linux
>pre-built version)
> To: "Caret, SureFit, and SuMS software users"
>
> Message-ID:
><50425.68.94.88.238.1246069010.squir...@brainvis.wustl.edu>
> Content-Type: text/plain;charset=iso-8859-1
>
> Enter "caret5 -help" at the command line.  There is an option like
> --Cleanlooks or something like that that makes me happy with Caret  
> on my
> Linux desktop.  Give it a shot.
>
> If it makes you happy, too, consider aliasing "caret" to "caret5
> --Cleanlooks" (or whatever the option actually is).  I'm not at a  
> computer
> that has Caret installed.  Shocking, I know.
> Thanks a lot for the information
>
> I gave it a try on the command-line option
> That did a great improvement on the layout style but the problem is  
> still there
> Maybe a picture can make my point more straightforward:
> http://img151.imageshack.us/img151/6825/rect3170.png
> Red dotted-boxes show where those truncated items are.
> Apparently, changing GUI style cannot alleviate the problem.
>
>
> > Dear Caret experts
> >
> > I tried Caret versions of 5.61 and 5.611 on my linux PC (OpenSUSE  
> 11.1
> > 64-bit edition).
> > They got the same problem that makes items on menubar truncated.
> > For example, the 3rd item under the "Surface" menu now looks like  
> "Convert
> > Main Window Surface to Segmenta".
> > Even though Caret GUI layout is controlled by Qt but there is no  
> way to
> > change its layout style with qtconfig.
> > This is quite annoying and prevents me from knowing what a button's
> > function
> > is by reading the text on it.
> >
> > Does anyone know how to fix it?
> > ___
> > caret-users mailing list
> > caret-users@brainvis.wustl.edu
> > http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >
>
> ___
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Re: [caret-users] Sections and MRIs

[John Harwell]

On Jun 26, 2009, at 8:59 PM, Donna Dierker wrote:

>> Subject: Sections and MRIs
>> From: "Peter L. Carras" 
>> Date: Fri, 26 Jun 2009 18:43:04 -0400
>> To: caret-users@brainvis.wustl.edu
>>
>> To: caret-users@brainvis.wustl.edu
>>
>>
>> Hello,
>>
>> I recently started using CARET (v5.61).  I have had some success, but
>> also a few questions that do not seem to be covered in the tutorials.
>> We have macaque brains with both MRI images and histological
>> sections.  The layer four contours for the sections of a left frontal
>> cortex were traced in MDPlot.  I have successfully imported the
>> contours into CARET, along with the labeled neurons found in each
>> section, and saved them as a spec file.  I also opened the MRI image
>> of the whole head in CARET, segmented it, and saved the left cortical
>> surface as another spec file.
>>
>> Q 1 - Is it possible to display the labeled neurons from the section
>> data on the MRI image of the complete cortex?  If so, how would I go
>> about doing this?  The histological sections were cut in the coronal
>> plane, and extend caudally only to the posterior commissure.

You will need to save the cells into a cell file and then load the  
cell file as a volume cell file.

* Load your data files including the cells and the MRI volume.
* Select File Menu->Save Data File to Display the Save Data FIle Dialog.
* Set the File Type to "Cell Files (*.cell)".
* At the bottom of the dialog, set "Cells Associated With Surface" to  
the fiducial (anatomical) surface.
* Enter a File Name (volume_cells.cell) and press the Save button.
* Select File Menu->Open Data File to display the Open Data File dialog.
* Set the File Type to "Cell Files - Volume (*.cell)".
* Select the cell file that was saved in a previous step and press the  
Open button.
* Display the volume in the Main Window.
* Press the Toolbar's "D/C" button to display the Display Control.
* Set the Page Selection to "Cell Main".
* Check the box labeled "Show Volume Cells".

As long as the surface and volume are aligned, the cells should appear  
over the volume slices.  In your Q3 you mention rotating the volume.   
This could be an issue for proper display of cells over volume slices.

>> Q 2 - When the contours were originally drawn, successive sections
>> were aligned on the dorsal-medial boundary of each section.  The
>> cortical fiducial surface as reconstructed by CARET is therefore
>> somewhat distorted - the sulci are visible but the dorsal edge of the
>> medial wall is flat rather than curved.  Will this cause the labeled
>> neurons to appear in incorrect locations when they are displayed on
>> the MRI-based surface?  If so, can you suggest a way to correct the
>> surface (short of re-tracing all 390 sections)?
>>
>> Q 3 - The SureFit segmentation algorithms were unable to successfully
>> operate on the MRI image, even when I tried varying the default gray
>> matter and white matter peak values.   Typically, the  program  
>> stopped
>> and reported an error in the eye fat segmentation step, or an error  
>> in
>> hindbrain segmentation.  When I de-selected those steps, CARET  
>> crashed
>> when determining layer 4 or filling the ventricles. I ended up
>> segmenting most of the brain manually.  Do you have advice on how to
>> increase the likelihood that SureFit will succeed in segmenting a
>> macaque MRI image?  The MPRAGE scan was done on a 3T Siemens Allegra
>> scanner with 0.7 mm isotropic voxels, and was rotated in CARET to LPI
>> orientation.
>>
>> Q 4 - Is it possible within CARET to convert the map of labeled
>> neurons (shown as contour cells on the fiducial surface) to a map of
>> cell density?

You will need a flat surface.  You will need to project the cells  
(Layers Menu->Cells->Project Fiducial Cells) with the fiducial surface  
in the main window.  Switch the display to the flat surface which now  
has cells on it as a result of cell projection.  Select Layers Menu- 
 >Cells->Convert Cell Density to Metric.  Use the Display Control to  
remove the cells and set the Surface Primary Overlay to Metric.

>>
>> Q 5 - In addition to the data on macaques, we also have anatomical  
>> and
>> MRI data from new world monkeys (Cebus apella).  Do you anticipate
>> adding Cebus to the list of species in the Metadata category?

We can add cebus to the list.  I don't believe any of the operations  
in Caret examine the species other than the automatic naming of new  
files.

>>
>>
>>
>> Your advice or assistance would be much appreciated.

Re: [caret-users] caret5 - (winxp and vista) - open data file / hanging ... /out of memory/ By Kure

[John Harwell]

Hello,

The message "MultiByteToWideChar: Cannot convert multibyte text" is  
produced by the QT platform independent user-interface software.

I changed the character set on one of our older Mac computers to  
simplified Chinese.  However, the date still appears in appears in  
English and I am unable to reproduce the crash.

Many of Caret's data file are written in pure ASCII text and my guess  
is that the non-English characters sets cause problems when trying to  
convert a multi-byte (unicode) character to an ASCII character.  One  
possible solution is to go to the Caret Preferences Dialog (Available  
from the Caret menu on Macs and the File Menu on Windows).  On the  
Preferences dialog, press the File tab button.  In the File Write  
Format section, set Highest Priority to XML.  Press the Apply button  
and then the Close button.  Some of Caret's data files, such as the  
Spec File, can be written in XML which should be able to support the  
multi-byte characters.  If this fails, the only solution is to use the  
English character set when running caret.

John


On Jun 22, 2009, at 9:00 AM, midoli wrote:

> Hi, Donna:
>
> Thanks for your patience.
>
> I read the old thread, and used the debug mode to make a screen print:
> http://midodo.net/neuro/caret_debug.gif
>
> I think ... this is a double-byte languages issue (Chinese,  
> Japanese, Korean )
> and maybe it happens in both Windows and Mac, especially when  
> creates a new spec file.
>
> Sincerely,
>
> Midoli :-)
>
>
> 2009/6/22 Donna Dierker 
> Kure and Midoli,
>
> First, thank you both for the excellent detail provided below. It  
> sheds
> a lot of light on the problem.
>
> Second, I do recall another thread where language issues caused  
> similar
> problems:
>
> http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg01635.html
>
> Unfortunately, I don't have a solution, but I do think this  
> information
> will help John understand what is going on.
>
> Donna
>
> On 06/21/2009 04:25 AM, kaiwu wrote:
> > Hi, I'm also a beginner of Caret, and I met almost the same  
> problem as the below message mentioned.
> > +++ 
> 
> > From: midoli 
> > To: "Caret, SureFit, and SuMS software users"
> >   
> > Message-ID:
> >   <958263d50906201929r6bcc4759ya482a3cdac46a...@mail.gmail.com>
> > +++ 
> 
> > I installed the caret5.61 in both my computer with WinXp Chinese  
> edition and Vista Japanese edition, respectively.
> > When I open a spec file, i.e. the spec file  
> "PALS_B12.RIGHT.MCW_2008_06.73730.spec" in the  
> "Caret5_Quick_Start_June_2008_Data" files, it alway display  
> "opening" and then prompt "out of memory" finally.
> > I don't know how to solve this problem.
> > Your help would be greatly appreciated.
> >
> > Kure
> >
> > === 2009-06-21 14:45:36 As you wrote：===
> >
> >
> >> Send caret-users mailing list submissions to
> >>  caret-users@brainvis.wustl.edu
> >>
> >> To subscribe or unsubscribe via the World Wide Web, visit
> >>  http://brainvis.wustl.edu/mailman/listinfo/caret-users
> >> or, via email, send a message with subject or body 'help' to
> >>  caret-users-requ...@brainvis.wustl.edu
> >>
> >> You can reach the person managing the list at
> >>  caret-users-ow...@brainvis.wustl.edu
> >>
> >> When replying, please edit your Subject line so it is more specific
> >> than "Re: Contents of caret-users digest..."
> >>
> >>
> >> Today's Topics:
> >>
> >>   1. Re: caret5 - (macosx) - open data file / hanging .../
> >>  reinstall is useless.. (midoli)
> >>
> >>
> >>  
> --
> >>
> >> Message: 1
> >> Date: Sun, 21 Jun 2009 10:29:25 +0800
> >> From: midoli 
> >> Subject: Re: [caret-users] caret5 - (macosx) - open data file /
> >>  hanging ... / reinstall is useless..
> >> To: "Caret, SureFit, and SuMS software users"
> >>  
> >> Message-ID:
> >>  <958263d50906201929r6bcc4759ya482a3cdac46a...@mail.gmail.com>
> >> Content-Type: text/plain; charset="iso-2022-jp"
> >>
> >> Thank you for the reply. The data file was on local hard disk,  
> not accessed
> >> via netw

Re: [caret-users] caret5 - (macosx) - open data file / hanging ... / reinstall is useless..

[John Harwell]

Midoli,

Which version of OS X is installed on your Mac (Apple Menu->About this  
Mac will tell you)?  We know that Caret will not run on versions prior  
to 10.4.

John



On Jun 12, 2009, at 8:57 PM, midoli wrote:

> Thanks for these kind suggestions.
>
> In fact, my Carot was broken down after my stupid operation.
> Everytime I open it, it seems to do the wrong process automatically  
> then crashes. I have tried to reinstall it and it still keeps  
> crashing.
> How could I kill the fail process clearly?
> If I can't kill it clearly, I will reinstall the MacOSX to repair  
> the Carot and then follow suggestions.
>
> Thanks,
> Midoli :-)
>
>
> On Sat, Jun 13, 2009 at 2:03 AM, Donna Dierker  > wrote:
> If you don't have AFNI installed, you can upload your .hdr here, and I
> can try mayo_analyze on my end:
>
> http://pulvinar.wustl.edu/cgi-bin/upload.cgi
>
> If you upload the .img file, too, I can try opening it in Caret.
>
> On 06/12/2009 11:43 AM, John Harwell wrote:
> > If you tried to load the "img" file, caret will ask the user for the
> > type of file.  Do not select the img file.
> >
> > Try selecting and loading the "hdr" file.  If caret is getting stuck
> > loading the file, then there is probably a problem the with hdr/img
> > files, most likely the byte order is incorrect so that dimensions
> > appear enormous to Caret.
> >
> > How were the hdr/img files created?
> >
> > If you have AFNI installed, try running "mayo_analyze  > file>".  What is the output?
> >
> > On Jun 12, 2009, at 9:37 AM, midoli wrote:
> >
> >
> >> Hi, All
> >>
> >> I'm just beginning to use Caret.
> >>
> >> I installed Caret5 in Mac OS.
> >> I used "File/Open Data File" to upload .hdr or .img file (sorry, I
> >> forgot which one I chose.) and it was hanging.
> >> The cursor kept on showing "processing" status, I waited for a long
> >> time... finally I used Ctrl+C to terminate Caret.
> >> I reopened Caret, it still showed "processing" status at the  
> opening
> >> time, I had no chance to do anything.
> >> I tried to restart OS, even reinstall Caret in a different
> >> directory these efforts were in vain.
> >>
> >> Did Caret hide something outside Caret's directory?
> >> How could I kill this fail process clearly and use Caret again?
> >>
> >> Thank you. :-)
> >>
> >> Shih-Chuan Chen.
>
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Re: [caret-users] caret5 - (macosx) - open data file / hanging ... / reinstall is useless..

[John Harwell]

If you tried to load the "img" file, caret will ask the user for the  
type of file.  Do not select the img file.

Try selecting and loading the "hdr" file.  If caret is getting stuck  
loading the file, then there is probably a problem the with hdr/img  
files, most likely the byte order is incorrect so that dimensions  
appear enormous to Caret.

How were the hdr/img files created?

If you have AFNI installed, try running "mayo_analyze ".  What is the output?

On Jun 12, 2009, at 9:37 AM, midoli wrote:

> Hi, All
>
> I'm just beginning to use Caret.
>
> I installed Caret5 in Mac OS.
> I used "File/Open Data File" to upload .hdr or .img file (sorry, I  
> forgot which one I chose.) and it was hanging.
> The cursor kept on showing "processing" status, I waited for a long  
> time... finally I used Ctrl+C to terminate Caret.
> I reopened Caret, it still showed "processing" status at the opening  
> time, I had no chance to do anything.
> I tried to restart OS, even reinstall Caret in a different  
> directory these efforts were in vain.
>
> Did Caret hide something outside Caret's directory?
> How could I kill this fail process clearly and use Caret again?
>
> Thank you. :-)
>
> Shih-Chuan Chen.
> ___
> caret-users mailing list
> caret-users@brainvis.wustl.edu
> http://brainvis.wustl.edu/mailman/listinfo/caret-users

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Re: [caret-users] MedialWall and BA40

[John Harwell]

Traci,

Select Attributes Menu->Paint->Assign Paint Names and Properties.

In the dialog, scroll to find BA40.  Press the button labeled BA40,  
change the name and press the OK button.  If you get a message that  
the name already exists, press the "R" button in the row for BA40 and  
select the medial wall name.  Lastly, save the paint file.

John



On Jun 11, 2009, at 11:05 AM, Sandoval, Traci I wrote:

> Hi Donna, Thank you for your response, but it did not seem to work.  
> I have attached a pic for your viewing pleasure, while it changes  
> the color of the medial wall, when you click it, it still states in  
> the identify window that is it BA 40? Additionally, I tried to  
> change the color of the medial wall before I ran deformation and it  
> changed it back to red and BA40? Thank you
>
>
> -Original Message-
> From: caret-users-boun...@brainvis.wustl.edu on behalf of Donna  
> Dierker
> Sent: Thu 6/11/2009 8:41 AM
> To: caret-users
> Subject: [caret-users] MedialWall and BA40
>
> Traci,
>
> I don't understand why the message below bounced.  Nor do I really
> understand how the paint indices got mixed up.
>
> But you should not need to re-draw the medial wall.  Do this:
>
> Surface: Region of interest, selection source Paint, select Brodmann. 
> 40
>
> Select node with Mouse, and click in the medial wall.
>
> Press select nodes and then Remove Islands
>
> Next
>
> Assign Paint: Column Brodmann
> Assign Name MEDIAL.WALL
>
> File: Save Data File: Paint
>
> Donna
>
>  Original Message 
>
> Subject:
> MedialWall and BA40
> From:
> "Sandoval, Traci I" 
> Date:
> Wed, 10 Jun 2009 16:34:07 -0500
> To:
> 
>
> Hello, I noticed that the medial wall is being defined as brodmann's
> area 40, I am guessing it is because they have the same color assigned
> to them. Is there a quick fix for this? Or do I need to re-draw the
> medial wall and re-assign as something else? Thank you for your
> continued help.Traci
>
> Traci Sandoval
> NeuroPychometric Research Lab
> Center for Brain Health
> University of Texas at Dallas
> University of Texas, Southwestern
>
>
>
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>
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Re: [caret-users] VTK 5.2+ compile fails

[John Harwell]

Steve,

What is the error you are receiving when trying to compile Caret?

Problems with newer versions of VTK are not unusual and I continue to  
use 5.0.2.  Plus, I have never been fond of cmake.  In any case, I  
have made a copy of VTK-5.0.2 available at 
"http://brainvis.wustl.edu/wiki_linked_files/caret_files/vtk-5.0.2.zip 
".  There is now a link to this version of VTK on from 
"http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/source_code/source_code.html
 
".  My desire is to remove VTK from Caret but VTK provides some  
complex algorithms (polygon decimation and surface reconstruction)  
that we need.

The bug report (http://bugs.donarmstrong.com/cgi-bin/bugreport.cgi?bug=518640 
) was probably resolved by a Caret user  (Michael Hanke) that builds  
Caret for Debian Linux.

In general, due to all of these compilation problems, we encourage the  
use of the compiled versions of Caret.

Good luck.

---
John Harwell
j...@brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On May 26, 2009, at 8:58 PM, Steve White (RMG) wrote:

> Hi
>
> I’m new to Caret and  trying to build in Vista from scratch. I’ve  
> followed (I think) all the instructions 
> onhttp://brainvis.wustl.edu/CaretHelpAccount/caret5_help/source_code/source_code.html
>  
>  but (besides having problems running the compiled versions of QT w/ 
> o recompiling) can’t get past the issue described here 
> http://bugs.donarmstrong.com/cgi-bin/bugreport.cgi?bug=518640 
>  – namely it appears to be barfing because I have a later version of  
> VTK than 5.0 – namely 5.4 – and no version earlier than 5.2 is  
> available online.
>
> The bug above indicates this issue is ‘resolved’. What patch can I  
> load in Vista to resolve this issue? Thanks
>
> Steve
>
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Re: [caret-users] Caret command line question

[John Harwell]

Patrick,

There is no command line option for performing this operation.  You  
will need to use the caret5 GUI for this operation.

John Harwell

On May 18, 2009, at 9:43 AM, Patrick De Mazière wrote:

> Hello,
>
> I want to create an RGB paint file using three metric files. The  
> metric files
> are created by mapping functional volumes onto a flat map. Since I  
> have to
> create more than a dozen of RGB paint files, I like to know how I  
> can do this
> using the command line interface, since this will speed up the  
> creation time
> considerably.
>
> Any suggestion will be welcome,
> Many thanks in advance !
>
> Best,
> Patrick
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Re: [caret-users] generating segmentation

[John Harwell]

The SureFit algorithm is complex algorithm that identifies the  
cerebral cortex.  It is described in "Van Essen, D.C., Drury, H.A.,  
Dickson, J., Harwell, J., Hanlon, D., and Anderson, C.H. and (2001).  
An integrated software suite for surface-based analyses of cerebral  
cortex. Journal of American Medical Informatics Association .  
8:443-459".  This paper can be downloaded from 
"http://brainvis.wustl.edu/wiki/index.php/Lab:Publications 
" or http://www.jamia.org/cgi/content/abstract/8/5/443. If you are  
unable to get the full text version, I can make a PDF version  
available to you, just let me know.

The "Threshold Into Segmentation" menu item simply creates a  
segmentation using all voxels that have a value within the selected  
range of values.  It might be useful for segmenting a subcortical  
structure.

---
John Harwell
j...@brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Apr 17, 2009, at 4:31 AM, Raemaekers, M.A.H.L.L. (Mathijs) wrote:

> Hi,
>
> When generating a segmentation from a T1 image using 'surefit  
> operations (segmentations)' I get a different segmentation  then  
> when using 'Threshold into segmentation' from the volume menu. The  
> segmentation from the surefit operations is a lot smoother and a bit  
> dilated when setting the same grey-white matter boundary. I seem to  
> be unable to find out how exactly this is achieved. I tried using  
> the volume dilate and erode command after thresholding into  
> segmentation, but did not manage to get the same results.
>
> Kind regards,
> Mathijs Raemaekers
>
>
> **
> Mathijs Raemaekers
> Functional Neurobiology
> Utrecht University
> Padualaan 8
> 3584 CH Utrecht
> Netherlands
>
> tel: +31-30-2531904
> fax: +31-30-2532837
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Re: [caret-users] should "appy RGB paint L-toL, R-to-R Matching to Coord Files be checked?

[John Harwell]

On Apr 14, 2009, at 9:21 AM, Yune S. Lee wrote:

>
> Dear Caret users,
>
> I just converted three Metric to one RGB paint file, but not sure if I
> should leave "Apply RGB paint L-toL, R-to-R Matching to Coord Files"
> unchecked or not in the RGB paint selection page.
> For default setting, it was unchecked, but  I'm wondering what it
> exactly is for. Any help would be appreciated.
>

Some of the user-interface components provide tooltips including the  
"Apply RGB paint L...".  If you place the mouse over a control and do  
not move the mouse for a few seconds a tooltip appears describing the  
control.  Look for the section titled "Surface Coloration Applies to  
Group" in 
"http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/dialogs/display_control_dialog.html
 
" for more information about L-to-L R-to-R.


On Apr 14, 2009, at 10:14 AM, Yune S. Lee wrote:

>
> Dear Caret users,
>
> I'm wondering the voxel XYZ coordinate is based on MNI or Taliarach
> coordinate.
> Also, it always shows the first floating value '.5' (e.g. 60.5, -47.5,
> 05.5) regardless and haven't seen the integer coordinates.
> Is there any particular reason why the coordinates end with 0.5?
> Any help would be appreciated.

We report the coordinate at the center of the voxel.  If the volume is  
in MNI stereotaxic space, it is an MNI coordinate.  If the volume is  
in a Talairach space, it is a talairach coordinate.  If you are  
looking for the voxel indices that identify the slice indices, they  
are integers listed as IJK.


John
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Re: [caret-users] Q) What could be the same as secondary underlay in overlay/underlay-surface page?

[John Harwell]

Metric is listed only if there is metric data loaded.

Did you load metric data as directed on page 24, "Press Toolbar: Spec  
then Spec File: Metric, open the
PALS_TUTORIAL.RIGHT.COMPOSITE.73730.metric file"?


On Apr 8, 2009, at 11:06 AM, Yune S. Lee wrote:

> Many thanks for your help with the screen capture.
> I suppose the layout of PC is different from mac as I don't see the  
> Metric in the data type.
> Enclosed is the screen capture of mine.
> Let me know what other alternative option I can choose.
>
> thanks,
> YSL
>
>
>
> John Harwell wrote:
>>
>>
>>
>> On the Display Control Overlay/Underlay - Surface page is a section  
>> with the title "Secondary Overlay".  In it, set the Data Type to  
>> Metric and controls for selecting the Display Column (metric  
>> column) and the Threshold Column will appear.
>>
>>
>>
>> 
>>
>>
>> John
>>
>>
>> On Apr 8, 2009, at 10:07 AM, Yune S. Lee wrote:
>>
>>>
>>> Hello,
>>> I'm trying to find the metric pulldown menu in the
>>> overlay/underlay-surface page and select AFM_BURTON_04_Vibrotactile_
>>> EARLY_BLIND) by following page 24 of the tutorial (1.22.2).
>>> Yet, I guess the secondary underlay no longer exists in the newer
>>> version and wonder how I instead select the file.
>>> Your help would be appreciated.
>>>
>>> Thanks,
>>> YSL
>>>
>>>
>>>
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>>>
>>
>>
>>
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>
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Re: [caret-users] unable to open spec file with an error message

[John Harwell]

That error message is caused deep inside the QT user-interface library  
that we use.  My only guess is that the computer is using a non- 
english character set and the characters are being processed  
incorrectly.

John

On Mar 31, 2009, at 1:49 PM, Donna Dierker wrote:

> YSL is still having posting/subscription issues which we are working  
> to
> address.
>
> Meanwhile, I am posting YSL's problem, which I have not encountered.
>
>> I'm not able to open .spec file and the caret command spits out a
>> message: MultiByteToWideChar: Cannot convert multibyte text.
>> Does anybody know why it happened?
>> I'm using caret in PC, by the way.
> Just confirming, YSL:  This happens when you double-click this file in
> Windows:
>
>   MY_CARET_DISTRIBUTION_PARENT_DIRECTORY/caret/bin_windows/caret5.exe
>
> Right?
>
> Donna
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Re: [caret-users] [caret] out of memory when loading inflated lateral view

[John Harwell]

My only guess is that one of the data files is corrupted.

Go to the File Menu and select Preferences.  Go to the Debug Tab and  
check the box next to Debug Enabled.   Now load your spec file and its  
data files.  As files are loaded, they will be listed in the DOS  
window.  What is printed in the window (screen capture)?

John Harwell

On Mar 31, 2009, at 4:08 PM, Yune S. Lee wrote:

> Dear Caret users,
> I'm a newbie for the caret.
> I get an "out of memory" error message when loading an inflated,  
> lateral view after opening PALS_B12.RIGHT.DEMO.scene in the tutorial  
> folder.
> As my pc  has 4GB memory and it is a brand new workstation, I'm not  
> sure why this is not capable of loading the file.
> I even tried again after turning off all other softwares but caret,  
> but still didn't work.
> Enclosed is the screen shot in case it might be helpful.
> Any help would be appreciated.
>
> Thanks,
> YSL
>
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Re: [caret-users] Quick projection of foci?

[John Harwell]

Alex,

I think the format you are trying to use is out of date.  I have added  
some information about reading foci from a spreadsheet at 
http://brainvis.wustl.edu/wiki/index.php/Caret:Operations/Foci 
.

---
John Harwell
j...@brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Mar 30, 2009, at 8:30 AM, Alex Fornito wrote:

> I have had a look at those tutorials, but I was hoping to bypass the  
> whole
> meta-data entry. All other potential solutions do not seem to do the  
> trick.
> I have noticed one thing though. In following the dated guide I  
> cited in my
> first email, I read a csv spreadsheet containing the foci into Caret  
> that
> had the following format:
>
> tag-version 1
> tag-number-of-cells 20
> tag-number-of-comments 3
> tag-BEGIN-DATA
> 0 x y z Study1 0
> 1 x y z Study1 0
> 2 x y z Study2 1
> 3 x y z Study2 1
> ...
> 0 SPM2
> 1 SPM99
>
> In the Map Stereotaxic focus dialog, I then assigned the stereotaxic  
> space
> in the 'Studies' dialog based on on the labelling at the bottom  
> (e.g., 0 =
> SPM2, 1=SPM99). I cliked 'Apply' for each focus and then tried to  
> project
> them using Project Foci to PALS atlas.
> It seemed to progress to completion without errors, but I cannot  
> visualize
> the foci. I've noticed however, that if I close Caret, re-open it  
> then try
> Project Foci to PALS atlas again, it tells me that the foci do not  
> have an
> associated stereotaxic space. I'm guessing there is something wrong  
> in the
> way I'm assigning the space.
>
>
>
> On 30/03/2009 13:49, "Donna Dierker"  wrote:
>
>> Hi Alex,
>>
>> That thread is pretty old, and David has been focusing (it pains me  
>> to
>> gratify his penchant for bad puns) a lot of effort on this subject.
>>
>> Have you seen these tutorials:
>>
>> http://sumsdb.wustl.edu/sums/stereotaxictocaretfoci.do
>>
>> Three things come to mind:
>>
>> * On the D/C menu, make sure the foci radio button at the very  
>> bottom of
>> the overlay/underlay - surface page (or Foci main page) is toggled  
>> on.
>>
>> * Make sure you have a focicolor file loaded
>> (http://brainvis.wustl.edu/CaretHelpAccount/caret5_help/file_formats/file_form
>> ats.html#fociColorFile)
>>
>> * Make sure the fiducial surface you have loaded in the main window  
>> is
>> in the same stereotaxic space as the foci.
>>
>> David may chime in, but I'm not sure when he returns from Germany.
>>
>> Donna
>>
>> On 03/30/2009 07:01 AM, Alex Fornito wrote:
>>> Hi,
>>> I'm trying to project some foci onto the PALS surface to get a quick
>>> impression of activation peak locations. I've glanced through the  
>>> tutorials
>>> and they described a fairly labour-intensive process requiring the  
>>> entry of
>>> lots of different data about each study. At this stage, I am not  
>>> planning on
>>> doing a formal meta-analysis and would just like to get obtain  
>>> some quick
>>> visualizations. To this end, I was hoping to import data from a  
>>> spreadsheet
>>> for visualization.  I followed the instructions posted on the  
>>> following
>>> mailing list thread
>>>
>>> http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg00982.html
>>>
>>> But, after following the process, I cannot visualize the foci.  
>>> That is,
>>> while Caret seems to read the data ok, and I can see the foci  
>>> details in the
>>> D/C, I can't actually see them on the surface.
>>> Is there perhaps some extra step that I have missed?
>>>
>>> Thanks for your help,
>>> Alex
>>>
>>>
>>>
>>
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>
> -- 
>
> Alex Fornito
> CJ Martin Post-Doctoral Fellow
> Brain Mapping Unit
> Department of Psychiatry
> University of Cambridge
> Downing Site
> Downing St, Cambridge
> UK CB2 3EB
>
> Email:af...@cam.ac.uk
> Phone:+44 (0) 1223 764670
> Fax:+44 (0) 1223 336581
>
> Australian Details:
>
> Melbourne Neuropsychiatry Centre
> National Neuroscience Facility
> Levels 1 & 2, Alan Gilbert Building
> 161 Barry St
> Carlton South 3053
> Victoria, Australia
>
> Email:forni...@unimelb.edu.au
> Phone:+61 3 8344 1861
> Fax:+61 3 9348 0469
>
>
>
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Re: [caret-users] question for caret

[John Harwell]

How are you mapping the volume?  To the PALS atlas or to an individual?

On what surface are you trying to view the results?  Is it a PALS  
surface?  If so, it will have the number 73730 (the number of nodes)  
in its name.

You can also load the surface into Caret and then map the volume using  
Map to Caret instead of Map to Atlas.

---
John Harwell
j...@brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Mar 27, 2009, at 9:23 AM, Jinhui Wang wrote:

> Dear John Harwell,
> Thank you for your answers very much. AAL template is in the MNI  
> stereotaxic
> space (here it is a nifti format of spm5).
>
> I have seen section 5.1 and tried every step as what the tutorial  
> tells.
>
> Following the suggestion in the tutouial, i don't run the mapping  
> algorithm and use the pre-computed  ***.metric in the result/ 
> subdirectory to view the result which is as a example. Everything  
> works. However, i also try to run the mapping algorithm to generate  
> new metric files and use them to view the reuslts. Unfortunately,  
> when i choose file/open data file and specify the new generated  
> metric files, a dialog box appear name "choose column to load"? What  
> does this mean?  And if i ignore it and press ok, an error happen  
> for the differnt number of nodes contained between the metric file  
> and the **coord file.
>
>  God. Please give me a hand. ^_^
>
>
> 2009/3/27 John Harwell 
>
> Instructions on how to use the PALS atlas and how to map functional
> volumes to the PALS atlas is available at 
> http://brainvis.wustl.edu/wiki/index.php/Caret:Documentation
> .  Download the Caret 5.5 Tutorial - The Basics (including PALS
> atlas).  Section 5.1 contains instructions on how to map a functional
> volume to the PALS atlas surfaces.  The human PALS atlas data set is
> available at http://sumsdb.wustl.edu/sums/humanpalsmore.do.
>
> I am not familiar with the AAL template.  Do you know the stereotaxic
> space of AAL?  Caret currently supports 711-2x, AFNI, FLIRT, MRITOTAL,
> SPM2, SPM5, SPM95, SPM96, and SPM99.
>
> Analyze files (hdr/img) typically lack the stereotaxic coordinate
> information needed to map the volume to the surface.
>
> ---
> John Harwell
> j...@brainvis.wustl.edu
>
> Department of Anatomy and Neurobiology
> Washington University School of Medicine
> 660 S. Euclid Ave   Box 8108
> Saint Louis, MO 63110
>
>
>
>
> On Mar 26, 2009, at 9:41 PM, Jinhui Wang wrote:
>
> > Hi,
> > will you please give me some help on how to map AAL template (.img
> > and .hdr; a public and used widely atlas) to PALS surface and
> > display it.   I have referred to some tutorial but don't solve it
> > yet.   Need i create some additional files?
> >
> > Sincerely
> >
> > --
> > Jin-hui Wang
> > State Key Laboratory of Cognitive Neuroscience and Learning,
> > Beijing Normal University
> > Add: No.19 Xinjiekouwai Street,
> > Beijing, China. 100875
> > Tel: +86 10 58802036
> > Fax: +86 10 58806154
> > E-mail:  wjh...@gmail.com
> >wjh122...@yahoo.com.cn
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>
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>
>
>
> -- 
> Jin-hui Wang
> State Key Laboratory of Cognitive Neuroscience and Learning,
> Beijing Normal University
> Add: No.19 Xinjiekouwai Street,
> Beijing, China. 100875
> Tel: +86 10 58802036
> Fax: +86 10 58806154
> E-mail:  wjh...@gmail.com
>wjh122...@yahoo.com.cn
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Re: [caret-users] question for caret

[John Harwell]

Instructions on how to use the PALS atlas and how to map functional  
volumes to the PALS atlas is available at 
http://brainvis.wustl.edu/wiki/index.php/Caret:Documentation 
.  Download the Caret 5.5 Tutorial - The Basics (including PALS  
atlas).  Section 5.1 contains instructions on how to map a functional  
volume to the PALS atlas surfaces.  The human PALS atlas data set is  
available at http://sumsdb.wustl.edu/sums/humanpalsmore.do.

I am not familiar with the AAL template.  Do you know the stereotaxic  
space of AAL?  Caret currently supports 711-2x, AFNI, FLIRT, MRITOTAL,  
SPM2, SPM5, SPM95, SPM96, and SPM99.

Analyze files (hdr/img) typically lack the stereotaxic coordinate  
information needed to map the volume to the surface.

---
John Harwell
j...@brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Mar 26, 2009, at 9:41 PM, Jinhui Wang wrote:

> Hi,
> will you please give me some help on how to map AAL template (.img  
> and .hdr; a public and used widely atlas) to PALS surface and  
> display it.   I have referred to some tutorial but don't solve it  
> yet.   Need i create some additional files?
>
> Sincerely
>
> -- 
> Jin-hui Wang
> State Key Laboratory of Cognitive Neuroscience and Learning,
> Beijing Normal University
> Add: No.19 Xinjiekouwai Street,
> Beijing, China. 100875
> Tel: +86 10 58802036
> Fax: +86 10 58806154
> E-mail:  wjh...@gmail.com
>wjh122...@yahoo.com.cn
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Re: [caret-users] missing instructions

[John Harwell]

Mat,

Those tutorials were written long ago, for a very old version of  
Caret.  Instead, go to 
"http://brainvis.wustl.edu/wiki/index.php/Caret:Documentation 
" and download the tutorial "Caret 5.5 Tutorial - Segmentation,  
Flattening, and Registration".  This tutorial contains a section on  
surface flattening.

---
John Harwell
j...@brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Mar 19, 2009, at 12:22 PM, Matvey Bosis wrote:

>
> Hi
>
> I would like to display my retinotopy maps on a flattened brain,  
> using Caret.
>
> I was unable to find the corresponding instructions to go with the  
> sample datasets TUTORIAL_05_FLATTEN_PARTIAL_HEMISPHERE and  
> TUTORIAL_06_FLATTEN_FULL_HEMISPHERE.
>
> Perhaps you can reffer me to someone who uses Caret for the same  
> purpose as I?
>
> Many Thanks!
> Mat
>
>
>
>
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Re: [caret-users] [caret] what does voxel IJK for in identfiy window?

[John Harwell]

When an identification operation is performed in Caret, information  
about the location identified is printed to the Identify Window.

The IJK values are the slice indices of the voxel that was  
identified.  The XYZ values are the stereotaxic coordinates at the  
identified voxel.

For each functional volume that is loaded, the value from the voxel at  
the identified stereotaxic coordinate is printed.  The values are  
listed after the "Functional" label.

John Harwell

On Mar 17, 2009, at 9:46 AM, life1...@gmail.com wrote:

> Dear caret users,
>
> I'm wondering what voxel IJK means and what this is for?
> It looks like XYZ, very next to this is the MNI coordinate as shown  
> below.
> Also, can anyone tell me wht the strings of 0 at Functional?
> Any help would be apprecited.
>
>
> VOXEL (Functional) IJK (66, 68, 41) XYZ (44.0, 13.0, 8.0)
> Functional: 0.0 0.0 0.0 0.0 0.0 0.0 0.0 1.0 1.0 0.0 0.0 0.0 0.0 0.0
>
>
> Thanks,
> YSL___
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Re: [caret-users] Projection foci

[John Harwell]

Alex,

To project foci to the PALS atlas, the foci must be linked to studies  
with valid stereotaxic spaces.  The stereotaxic space determines which  
of the surfaces inside of the Caret distribution are used to project  
the focus.  Studies are edited using the Attributes Menu->Study  
Metadata->Edit Studies Dialog.  There is some documentation on this  
dialog at 
"http://brainmap.wustl.edu/caret/caret_help/dialogs/study_metadata.html 
".

Once studies have been entered, return to the Map Stereotaxic Focus  
Dialog and use the edit mode.  Pressing the Study Metadata Button  
allows one to choose the appropriate study for the focus.  After  
linking the study to the focus press the Apply button and the focus  
should be properly projected.

---
John Harwell
j...@brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Jan 14, 2009, at 3:48 PM, Alex Fornito wrote:

>
> Hi,
> I entered a few stereotactic foci manually and saved  
> the .foci, .fociproj,
> and .focicolor files.
> When I opened Caret up again and re-loaded the spec file, I was  
> unable to
> view the foci on the surface. I can see them in the foci windows of  
> the
> display control, but if I select Layers > foci > Foci projection to  
> PALS
> atlas, I get a message saying "These foci do not have associated  
> stereotaxic
> spaces: ..."
> I was wondering whether it is possible to visualize the foci again,  
> without
> entering them all again.
>
> Thanks,
> Alex
>
>
>
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Re: [caret-users] Flattening process with new caret version

[John Harwell]

Sofia,

When you installed caret v5.6, did you install the full distribution  
or just the executable?  The borders listed on the flattening dialog  
are contained in files located in the caret distribution's "data_files/ 
flatten_borders".  If you did not get the full distribution, try  
downloading and using it.

Another possibility is that you have the CARET5_HOME environment  
variable set.  This is only needed in very unusual circumstances so,  
if it is set, unset it.

---
John Harwell
j...@brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Jan 15, 2009, at 7:40 AM, Sofia Crespi wrote:

> Hi Donna
> I have a problem with the segmentation and flattening processes with  
> the new version (caret v5.6) I have downloaded.
> with the old version (5.5) I segmentated my volume, once the  
> segmentation process finished I corrected manually the topological  
> errors still present and finally I generated a final surface for  
> flattening.
> Then I used to select the Ellipsoid Surface, from the Surface Menu  
> and on the Flatten Full or Partial Hemisphere  Dialog I set the  
> Flattening type to Full Hemisphere (Ellipsoid) and Morph Sphere  
> finally I selected the Human Right (or left!) Standard Cuts as  
> Border Template Cuts.With my new caret version this last step is no  
> more possible.
> I can only choose between :
> 1. choose template Borders.But I do not know which Template  
> Borders I should select and where to find the template
> 2. Use currently loaded Ellipsoidal Borders, but if I choose this  
> second option caret tells me that Border Files contains no Borders.
> ???
>
> Can you help me?
> thank you in advance
> sofia
>
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Re: [caret-users] displaying several ROIs simultaneously

[John Harwell]

Binyam,

You will need to combine all of your ROIs into a single image.  For a  
paint volume, there are no controls for turning the individual paints  
(ROIs) on and off.  However, if you load the image as a probabilistic  
atlas volume, you can turn the ROIs on and off using the Display  
Control's Probabilistic Atlas - Volume Area page.

---
John Harwell
j...@brainvis.wustl.edu

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Dec 16, 2008, at 5:07 PM, Binyam Nardos wrote:

> Hi all,
> I am trying to display several ROIs simultaneously based on  
> WUNIL .ifh files as volume via  Attributes > map volumes to surfaces  
> > paint (ROI) or probabilistic data. I can get the individual ROIs  
> to show up fine as well as display up to three ROIs simultaneously  
> using paint as secondary and tertiary overlay. How does one get to  
> display multiple >3 ROI simultaneously. I've thought about  
> clustering my ROIs into one image first and then displaying them,  
> but this beats my purpose as I would like to turn some on/off etc  
> for easy identification purposes. If I recall, in a much older  
> version of CARET, this used to be possible via selecting multiple  
> ROIs simultaneously under Display control >paint selection.
>
> please advise,
>
> thank you,
> Binyam
>
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Re: [caret-users] Node to Voxel Mapping

[John Harwell]

Traci,

There is not a way to control the assignment of paint identifiers when  
creating the paint volumes.

However, if you combine all of the individual paint volumes into a  
"multi-volume" file, the paint indices will be synchronized.  You will  
need to use "caret_command", the command line tool included with the  
Caret distribution.  Specifically, you will need to run the command  
"caret_command -volume-file-combine".  Be sure to use the "-paint"  
option at the end of your command so that the paint names get  
synchronized.  If you still need each volume separately, you will need  
to load the multi-volume file into Caret and then save each of the  
volumes contained in the multi-volume file.


caret_command -volume-file-combine
VOLUME FILE COMBINE
   caret_command -volume-file-combine
  
  
  [additional-input-volume-files]
  [-paint]
  Combine the volumes into a single, multi-volume file.

  If the volumes are paint or probabilistic atlas volume
  files, the "-paint" option must be specified so that
  paint name indices are synchronized throughout all of
  the volumes.


Good luck.

---
John Harwell
[EMAIL PROTECTED]

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Dec 8, 2008, at 1:10 PM, Sandoval, Traci I wrote:

> Hello All,
>
> We’ve been trying to create volume ROIs from our surfaces.  We use  
> “copy surface paint column to paint volume” to create “node to voxel  
> mapping.”   The problem is that across hemispheres and subjects  
> different numbers get assigned to the paint ROIs in the volume  
> file.  Is there a way to control the numbers assigned?
>
> - Traci
>
> __
> Traci Sandoval
> Research Assistant
> School of Behavioral and Brain Sciences - University of Texas at  
> Dallas
> Center for BrainHealth - University of Texas at Dallas
> Department of Psychiatry - University of Texas Southwestern Medical  
> Center
>
>
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Re: [caret-users] install-caret

[John Harwell]

Did you download the caret source code, the C++ files (file  
caret_source*.zip) ?  Or, did you download the caret distribution  
(caret_distribution*.zip)?

If you downloaded the source code, you need to follow the instructions  
for building the source code 
(http://brainmap.wustl.edu/caret/caret_help/source_code/source_code.html 
).

If you have the distribution, the file "install-caret.sh" is located  
in the "caret" directory and only needs to be run on Unix/Linux to fix  
file permissions that sometimes get set incorrectly.  If caret5 runs,  
there is no need to run the script.

---
John Harwell
[EMAIL PROTECTED]

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Dec 5, 2008, at 12:53 PM, Siddharth Srivastava wrote:

> Hi List,
>i recently downloaded caret source, and wanted to build  
> it. As
> per the instructions, i was required to run the script install- 
> caret, but
> i am not able to find that script anywhere in the unzipped  
> distribution.
> Do i have to do something else before to generate this script?
> thanks,
> sid.
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Re: [caret-users] different number of nodes

[John Harwell]

Markus,

How did you map the volume to the surface?  It appears that you may  
have mapped it to the colin atlas which contains 71723 nodes.

Are you trying to view the results on the  
Human.SPM_T1_TEMPLATE.R.Fiducial.17856.coord surface (17856 nodes)?   
If so, this will not work as the metric file must have the same number  
of nodes as the surface.  If you want to view the functional data on  
the Human.SPM_T1_TEMPLATE.R.Fiducial.17856.coord surface, you will  
need to map the functional data to that surface.

Lastly, if you are mapping group results, we recommend the PALS atlas 
(http://sumsdb.wustl.edu/sums/humanpalsmore.do 
) for mapping and viewing.  For an individual, you need to map the  
functional volume to the individual's surface.

---
John Harwell
[EMAIL PROTECTED]

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Nov 24, 2008, at 8:24 AM, Markus Goldhacker wrote:

> Hello,
>
> I'm working with CARET for my physics diploma. Recently I had a  
> problem
> with mapping a contrast from SPM on a 3D-model. I got the following
> error:
>
> Error  map_data_2_COLIN_RIGHT_17_Nov_2008_12_17_42.metric:  contains a
> different number of nodes than
> Human.SPM_T1_TEMPLATE.R.Fiducial.17856.coord
>
> The volume-file was the SPM T1 template. I don't know what to do. What
> went wrong? How can I change the number of nodes? How can I make them
> equal?
>
> Thanks in advance!
>
> Kind regards
>
> Markus Goldhacker
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Re: [caret-users] flat surface deformation and metric file: how do i create metric file with nodes from flat surface only?

[John Harwell]

Quintino,

One thing you can try is to export the functional column to a  
FreeSurfer Functional File (extension ".w.asc").  On the File Menu- 
 >Save Data File Dialog, set the Filter to FreeSurfer Functional.   
This file contains two columns where the first column contains the  
node number and the second column contains the node's functional  
value.  Nodes are only listed if the functional value is non-zero.   
However, there is a bug in the current version of Caret in that it  
erroneously starts the file with zero values for all nodes which are  
then followed by the correct data containing nodes with non-zero  
functional values.  So, ignore the zero data.

Another alternative is running "caret_command -surface-topology- 
neighbors" with your flat surface's topology file.  This can help you  
identify nodes that are in your flat surface by listing nodes with  
neighbors.  Each line of the output contains a node number.  Following  
the node number, on the same line, are the connected neighbors of the  
node.

John Harwell

On Nov 6, 2008, at 10:07 AM, Donna Dierker wrote:

> Hi Quintino,
>
> Post to caret-users@brainvis.wustl.edu rather than
> [EMAIL PROTECTED]; the latter address is just  
> aliased
> to me, so if I'm out of the office, no one else will see your message.
> Posting to caret-users gets many more brains on your question.
>
> As far as I know, there is no way for Caret to output a metric file  
> that
> includes only a subset of nodes.  (It is possible this functionality  
> is
> supported in the GIFTI standard, and that Caret supports it; if so,  
> John
> Harwell will clarify.)
>
> The best you can do is zero out (or set to a number that is more
> obviously not sane, like -9) the nodes outside the flat  
> surface.  If
> you are visualizing your results on the flat surface, then the
> disconnected nodes won't be visible.  Likewise, you can assign the  
> same
> CUT topology file to your fiducial and/or inflated 3D surfaces, so  
> that
> those nodes are not visible.
>
> Finally, if you are using a third party software package like matlab  
> to
> manipulate your metric files, you could also use a paint file to
> identify nodes inside the surface or outside the surface.  Paint files
> are like metric files, except the nodal information is
> discrete/categorical/ROI vs continuous/scalar/functional.
>
> Donna
>
> On 11/06/2008 09:44 AM, Quintino Mano wrote:
>> Hi all,
>>
>> I'm in the process of deforming a flat surface, which is a selected
>> patch from the left occiptio-temporal cortex. In doing so, the
>> corresponding metric file is also deformed, which is great, but
>> unfortunately the resultant metric file includes nodes from the  
>> entire
>> hemisphere, and not just the nodes in my flat surface. Does anyone
>> know how to deform a metric file that is comprised of only nodes that
>> are contained in flat surface?
>>
>> Many thanks in advance!
>>
>> Quintino
>>
>
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Re: [caret-users] algorithm args backwards in caret_command?

[John Harwell]

Baylis,

You are right, the parameters are being read in reverse.

The problem involves the way the compiler processing arguments to a  
function.   When calling a function, the compiler processes the  
arguments from last to first.  So, if "function(a(), b(), c())" is  
called, the compiler calls c() then b() and then a() which explains  
the behavior you are seeing.


If you need an updated caret_command, let know which operating system  
you are using.


---
John Harwell
[EMAIL PROTECTED]

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Oct 13, 2008, at 5:30 PM, Baylis Shanks wrote:



Only the algorithm-specific parameters (of which  
METRIC_ENCLOSING_VOXEL has none) are reversed. caret_command -help- 
full contains the text:


[-g   gaussian-neighbor-cube-size (mm)
  sigma-norm
  sigma-tang
  norm below cutoff (mm)
  norm above cutoff (mm)
  tang-cutoff (mm)]

So, one would expect that the command "caret_command -volume-map-to- 
surface coord topo \"\" outfile METRIC_GAUSSIAN infile -g  
not_a_number 1 1 1 1 1" would cause an error in the ostensible first  
parameter, "gaussian-neighbor-cube-size". However, as detailed in my  
trace below, actually the error is reported in parameter ""Gaussian  
Tangent Cutoff".


Similarly, if you put an invalid parameter in the second position  
after -g, it should cause trouble with the parameter "sigma-norm",  
but actually the error is reported in parameter "Gaussian Norm Above  
Cutoff".


Similarly if you put an invalid parameter in the last position after  
-g.


Similarly, if you look at the column comments for a Gaussian  
algorithm-mapped metric file by using the "?" button in D/C, it  
seems like it read the algorithm-specific parameters in backwards.


sorry for being unclear before,
 thanks, bayle







Date: Mon, 13 Oct 2008 09:41:42 -0500
From: [EMAIL PROTECTED]
To: caret-users@brainvis.wustl.edu
Subject: Re: [caret-users] algorithm args backwards in caret_command?

Hi Bayle,

This command worked just fine for me:

caret_command -volume-map-to-surface test.scale.coord test.topo ""
test.out.metric METRIC_ENCLOSING_VOXEL test.nii

That is, I didn't get the errors you cite below; however, I did get  
the

patchiness described in your other message (see capture).

This usage matches my help output for this feature.

Donna

On 10/10/2008 08:43 PM, Baylis Shanks wrote:
It seems like caret_command is reading in algorithm arguments  
backwards (compared to the order they are listed in caret_command - 
help-full):



$ caret_command -volume-map-to-surface coord topo \"\" outfile  
METRIC_GAUSSIAN infile -g not_a_number 1 1 1 1 1


VOLUME MAP TO SURFACE ERROR: Error converting parameter named  
"Gaussian Tangent Cutoff" with value "not_a_number" to a float


[EMAIL PROTECTED]:~/aba/niis_layer$ caret_command -volume-map- 
to-surface coord topo \"\" outfile METRIC_GAUSSIAN infile -g 1  
not_a_number 1 1 1 1


VOLUME MAP TO SURFACE ERROR: Error converting parameter named  
"Gaussian Norm Above Cutoff" with value "not_a_number" to a float


[EMAIL PROTECTED]:~/aba/niis_layer$ caret_command -volume-map- 
to-surface coord topo \"\" outfile METRIC_GAUSSIAN infile -g 1 1 1  
1 1 not_a_number


VOLUME MAP TO SURFACE ERROR: Error converting parameter named  
"Guassian Neighbor Cube Size (mm)" with value "not_a_number" to a  
float




this isn't a big problem since you can just put the args in  
backwards, but just fyi


thanks,
 bayle
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Re: [caret-users] Problem viewing NIFTI volume file in 5.6

[John Harwell]

Baylis,

Previously, you discovered that Caret was not reading a NIFTI volume  
correctly in regards to the units and if only the qform coordinate  
space was used.  When you generated your surface, it must have been  
generated with a version of Caret that did not correctly read the  
volume as the surface's units are microns.  If you download updated  
versions of care5 and caret_command it should resolve your problem.   
You will need to either regenerate your surface, so that its units is  
millimeters, or scale the surface using Surface Menu->Transform->Scale  
with a value of 0.001 and save the coordinate file.


To verify that the surface and the volume are properly aligned, load  
both the volume and the surface into Caret and display the volume.   
Use the Display Control's Volume Surface Outline page to place an  
outline of the surface over the volume.


Updated versions of caret5 (caret5_exe_*.zip) and caret_command  
(caret_command_exe_*.zip) are available at http://brainmap.wustl.edu/pub/john/ 
.  Use the username "pub" and the password "download" to access the  
website.  Source code (caret_source.v5.6.zip) is also available.


---
John Harwell
[EMAIL PROTECTED]

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Oct 8, 2008, at 9:19 PM, Baylis Shanks wrote:



hello again,


When using caret_command to do a -volume-map-to-surface i seem to be  
getting a bunch of zeros in the output metric file with at least  
some mapping algorithms.


If i use caret_map_fmri version 5.51 I don't get zeros.

Specifically, the command that produces non-zeros is:

 caret_map_fmri -a EV -v test.nii -s test.spec test.topo test.coord - 
m test.metric


and the command that produces zeros is:

 caret_command -volume-map-to-surface test.coord test.topo \"\"  
test.metric METRIC_ENCLOSING_VOXEL test.nii


note that the .coord and .topo files that i am using in both cases  
were produced by Caret 5.51.



test.spec, test.topo, and test.coord are available at:

http://rapidshare.com/files/152231400/test.spec.html
http://rapidshare.com/files/152231401/test.topo.html
http://rapidshare.com/files/152231402/test.coord.html

test.nii is the same as before.

in case it's useful, in attempting (and failing) to debug the  
problem, i observed what may be inappropriate units either being fed  
to or generated by the function convertCoordinatesToVoxelIJK.  
details below



-



in debugging the problem, i noticed that in the file  
BrainModelVolumeToSurfaceMapper.cxx, in the function  
getNeighborsSubVolume (which is called by some mapping algorithms),  
there is a call to convertCoordinatesToVoxelIJK.  
convertCoordinatesToVoxelIJK always returns FALSE in my case because  
it thinks the coordinates it is given are out of bounds.


debugging convertCoordinatesToVoxelIJK, i notice that the numbers  
passed in as "xyz" seem to be in the thousands (i.e. numbers like  
4150.34 -- probably in units of microns) whereas the result of  
getOriginAtCornerOfVoxel are in units of millimeters. the units of  
"spacing" are also millimeters.


If, inside of convertCoordinatesToVoxelIJK, i temporarily replace  
the line:


const float d = xyz[i] - originCorner[i];

with

 const float d = (xyz[i]/1000) - (originCorner[i]);

then the output of convertCoordinatesToVoxelIJK is more reasonable  
(by which i mean, it doesn't return FALSE anymore). To me this  
suggests that the function convertCoordinatesToVoxelIJK should  
either be given its input in terms of millimeters, or should consult  
the header information and convert its input units if needed.


however, even with the temporary modification, the result of  
caret_command -volume-map-to-surface is zeros, so there must be  
something else also.


thanks,
 bayle








From: [EMAIL PROTECTED]
To: caret-users@brainvis.wustl.edu
Date: Tue, 23 Sep 2008 12:00:00 -0500
Subject: Re: [caret-users] Problem viewing NIFTI volume file in 5.6

Bayle,

There are two ways to describe the coordinate system in a NIFTI  
volume
by using the qform_code and the sform_code.  Your volume used only  
the
qform_code and Caret was processing it incorrectly.  Some changes  
have

been made and Caret now appears to read your volume correctly.

You can get an updated version of the caret5 executable from 
"http://brainmap.wustl.edu/pub/john/
".  Use the username "pub" and the password "download" to access the
website.  There are three zip files whose names begin with
"caret5_exe" that contain updated versions of caret5.  Download the
version appropriate for your operating system and install it.  On
Windows, place caret5.exe in you Caret installations "bin_windows"
directory.  On Linux, place caret5 i

Re: [caret-users] Problem with caret 5.1

[John Harwell]

Hello,

On March 26, 2007, Caret was updated to read NIFTI hdr/img files.   
Caret 5.1 was released in 2004.  Updating to the latest release of  
Caret should resolve your problem.


---
John Harwell
[EMAIL PROTECTED]

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Sep 26, 2008, at 10:57 AM, Donna Dierker wrote:

Not as far as I know, but I haven't tried.  If John made that  
enhancement, it would be in the change log (see caret page).


- Original Message 
From: Alireza Salamy <[EMAIL PROTECTED]>
To: Donna Dierker <[EMAIL PROTECTED]>
Cc: caret-users@brainvis.wustl.edu
Sent: Friday, September 26, 2008 8:21:43 AM
Subject: Re: [caret-users] Problem with caret 5.1

Hello,

what about the latest version of caret(5.6)?can it be feeded by  
Spm5.Img/hdr pair?


--- On Fri, 9/26/08, Donna Dierker <[EMAIL PROTECTED]>  
wrote:

From: Donna Dierker <[EMAIL PROTECTED]>
Subject: Re: [caret-users] Problem with caret 5.1
To: [EMAIL PROTECTED]
Date: Friday, September 26, 2008, 3:57 PM

Hi Alireza,

If you are feeding Caret a SPM5 .img/.hdr pair, rather than a .nii  
volume, this could happen.  Caret does not yet read NIfTI .img/.hdr  
pairs properly; however, if you write the volume as .nii, you'll  
have better luck.


Donna

- Original Message 
From: Alireza Salamy <[EMAIL PROTECTED]>
To: caret-users@brainvis.wustl.edu
Sent: Friday, September 26, 2008 3:51:40 AM
Subject: [caret-users] Problem with caret 5.1

Hello,

I am a new user,so sorry if this question sounds stupid.
I have a problem with caret 5.1.It does not actually show  my  
activation of any of the hemisphere.First I chose the spec file and  
then I choose map functional volume to matrix and then choose the  
selected metric by primary overlap option but nothing appears on my  
brain.I use SPM5 to make the image file.Could it be the reason of  
coordinate of SPM5(isn't it supported by this version of caret5.1)? 
shall I use the latest version?

Thanks in advance
/A


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Re: [caret-users] Problem viewing NIFTI volume file in 5.6

[John Harwell]

Bayle,

There are two ways to describe the coordinate system in a NIFTI volume  
by using the qform_code and the sform_code.  Your volume used only the  
qform_code and Caret was processing it incorrectly.  Some changes have  
been made and Caret now appears to read your volume correctly.


You can get an updated version of the caret5 executable from "http://brainmap.wustl.edu/pub/john/ 
".  Use the username "pub" and the password "download" to access the  
website.  There are three zip files whose names begin with  
"caret5_exe" that contain updated versions of caret5.  Download the  
version appropriate for your operating system and install it.  On  
Windows, place caret5.exe in you Caret installations "bin_windows"  
directory.  On Linux, place caret5 in you Caret installation's  
"bin_linux" directory.  On Mac OSX, place caret5.app in you Caret  
installation's "macosx_apps" directory.


---
John Harwell
[EMAIL PROTECTED]

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Sep 23, 2008, at 8:27 AM, Donna Dierker wrote:


Hi Bayle,

I removed your attachments and placed them in our upload directory,  
and

I am forwarding your reply to caret-users that got held up due to
message size constraints.  I let the first attachment you sent  
through,

because it was just a bit above the limit, but this message had three
volumes attached exceeding 2.5Mb total.  We don't want to fill up
everyone's inbox.

I'll try to have a look at this later today, but I wanted John Harwell
to get a look before he takes a few days off later this week.

Donna

 Original Message 
Subject:RE: [caret-users] Problem viewing NIFTI volume file in 5.6
Date:   Tue, 23 Sep 2008 01:21:10 +
From:   Baylis Shanks <[EMAIL PROTECTED]>
To: Caret, SureFit, and SuMS software users




hi,

thanks for looking into it.


When I view it in AFNI, I do see something that might be mouse cortex


yes, it's mouse cortex, and that is what it is supposed to look  
like :)



R-to-L extent:  5688.600 [L] -to-  5700.000 [L] -step- 0.200 mm  
[ 58

voxels]
A-to-P extent:  7786.800 [P] -to-  7800.000 [P] -step- 0.200 mm  
[ 67

voxels]
I-to-S extent: -2700.000 [I] -to- -2692.000 [I] -step- 0.200 mm  
[ 41

voxels]
...
If the voxdims are really cubic .2mm, which is consistent with the  
mousy
look of what AFNI shows, then the field of view should be 11.6x13.4  
mm

-- not what is shown above.


by "what is shown above", you meant this, right?

there are indeed supposed to be 58, 67, and 41 voxels along the R-L,  
A-P, and I-S directions. the value of the "dim" header field is  
[ 3   58   67   410000]  (i think -- that is the  
value that i tried to put in there, but bear in mind that since i  
created the file i could have written out the header incorrectly).


on to the displacement. i was trying to make the origin be the  
anterior commissure, which i believe to be near 5.7, 7.8, 2.7 mm.


what are the units of the numbers 5700, 7800, 2692? my intent was  
for them to be microns. the values of the NIFTI header fields  
qoffset_x, qoffset_y, qoffset_ z are (i think) -5700, -7800, and  
-2700 respectively. the value of the NIFTI header field xyzt_units  
is (i think) NIFTI_UNITS_MICRON. but perhaps the units of the  
qoffset_* fields were supposed to be units of millimeters?


5700-5688.6 is 11.4, which is pretty close to 11.6 (58*.2 = 11.6) --  
so it seems like 3dinfo is interpreting the 5700 as mm, and  
subtracting 11.4 mm from it to get the 5688.6.


so, i tried changing header fields but i haven't yet figured out how  
to completely fix the problem (read on for details).


before talking about that, i'd like to note something strange i  
noticed in the Caret's Volume Attributes Editor when viewing the  
original file that i included in the previous email, test.nii (when  
loading it as an Anatomy volume). The dialog shows the "Dimensions"  
as 1 in each direction, "Voxel Size" as 200, and Origin as -57, -78,  
and -27. This is odd, because one would think that the Voxel Size is  
correct and is displayed in units of microns, but one would think  
that Origin would be either -5700, -7800, -2700 (if the qoffset  
header fields are being read as microns and displayed as microns)  
-570, -780, -270 (if the qoffset header fields are being  
read as mm and displayed as microns), or it should be -5.7, -7.8,  
-2.7 (if the qoffset header fields are being read as microns and  
displayed as mm).


now, i will describe the results of trying to change some of the  
header fields, yielding new test files (attached).


first, i tried to simply scale the qoffset fields. I replaced -5700,  
-7800, -2700 with -5.7, -

Re: [caret-users] Caret crashes when trying to load different models

[John Harwell]

Eun,

The error report indicates that your Mac has a PowerPC processor  
(ppc).  While we build the Mac version of Caret so that it should run  
on both Intel and PowerPC Mac computers, a recent release crashed on  
PowerPC Macs (http://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg01432.html 
).  The crashes have not occurred with later builds of Caret.


Try downloading an update to Caret and see if it resolves the problem.

Go to "http://brainmap.wustl.edu/pub/john/";.  You will need to use the  
username "pub" and the password "download" to access the website.   
Download the file caret5_exe_osx.zip.  Place the downloaded file into  
your Caret installation's "macosx_apps" directory.  Rename the  
existing "caret5.app" and then unzip the downloaded file to create a  
new "caret5.app".


---
John Harwell
[EMAIL PROTECTED]

Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave   Box 8108
Saint Louis, MO 63110




On Aug 27, 2008, at 10:33 AM, Eun Young Choi wrote:


Hi everyone,

I'm having a problem loading different models (ie, inflated, flat,  
volume) of both the "Human PALS B12 For Stereotaxic Foci Analysis"  
and the atlas from Quick Start Tutorial 5.504. I can load the  
fiduciary model, but the program crashes when I try to open another  
model. I'm using Mac OS X Leopard, and I suspect this might have to  
do with the problem: I get the same problem on another Leopard  
computer and two other members of the lab using Tiger (the previous  
version of Mac OS X) have no problems. I've pasted the error report  
below.


Any help would be much appreciated.

Thanks,
Eun Young

Process: caret5 [44839]
Path:/Applications/caret/macosx_apps/caret5.app/Contents/ 
MacOS/caret5

Identifier:  caret5
Version: ??? (???)
Code Type:   PPC (Native)
Parent Process:  launchd [237]

Date/Time:   2008-08-26 12:18:02.724 -0400
OS Version:  Mac OS X 10.5.4 (9E17)
Report Version:  6

Exception Type:  EXC_BAD_ACCESS (SIGBUS)
Exception Codes: KERN_PROTECTION_FAILURE at 0x0008
Crashed Thread:  0

Thread 0 Crashed:
0   caret50x00eb6b64  
QwtPlotPicker::~QwtPlotPicker() + 1420916
1   caret50x00f0597c  
QwtPlotPicker::~QwtPlotPicker() + 1744012
2   caret50x00f070a0  
QwtPlotPicker::~QwtPlotPicker() + 1749936
3   caret50x0112b60c  
QwtPlotPicker::~QwtPlotPicker() + 3995932
4   caret50x01224d0c  
QwtPlotPicker::~QwtPlotPicker() + 5017628
5   caret50x012a5078  
QwtPlotPicker::~QwtPlotPicker() + 5542792
6   caret50x00e629c8  
QwtPlotPicker::~QwtPlotPicker() + 1076440
7   caret50x01207b00  
QwtPlotPicker::~QwtPlotPicker() + 4898320
8   caret50x00e2228c  
QwtPlotPicker::~QwtPlotPicker() + 812444
9   caret50x00e2520c  
QwtPlotPicker::~QwtPlotPicker() + 824604
10  caret50x013caa1c  
QwtPlotPicker::~QwtPlotPicker() + 6745388
11  caret50x00e8bb10  
QwtPlotPicker::~QwtPlotPicker() + 1244704
12  com.apple.HIToolbox   0x9009d3c8  
DispatchEventToHandlers(EventTargetRec*, OpaqueEventRef*,  
HandlerCallRec*) + 1484
13  com.apple.HIToolbox   0x9009c560  
SendEventToEventTargetInternal(OpaqueEventRef*,  
OpaqueEventTargetRef*, HandlerCallRec*) + 464
14  com.apple.HIToolbox   0x9009c37c  
SendEventToEventTargetWithOptions + 52
15  com.apple.HIToolbox   0x900c1120  
HIView::SendDraw(short, OpaqueGrafPtr*, __HIShape const*,  
CGContext*) + 400
16  com.apple.HIToolbox   0x900c0cb8  
HIView::RecursiveDrawComposited(__HIShape const*, unsigned long,  
HIView*, CGContext*, unsigned char, float) + 676
17  com.apple.HIToolbox   0x900c0db8  
HIView::RecursiveDrawComposited(__HIShape const*, unsigned long,  
HIView*, CGContext*, unsigned char, float) + 932
18  com.apple.HIToolbox   0x900c0db8  
HIView::RecursiveDrawComposited(__HIShape const*, unsigned long,  
HIView*, CGContext*, unsigned char, float) + 932
19  com.apple.HIToolbox   0x900c0db8  
HIView::RecursiveDrawComposited(__HIShape const*, unsigned long,  
HIView*, CGContext*, unsigned char, float) + 932
20  com.apple.HIToolbox   0x900c0db8  
HIView::RecursiveDrawComposited(__HIShape const*, unsigned long,  
HIView*, CGContext*, unsigned char, float) + 932
21  com.apple.HIToolbox   0x900bff60  
HIView::DrawComposited(short, OpaqueGrafPtr*, __HIShape const*,  
unsigned long, HIView*, CGContext*) + 644
22  com.apple.HIToolbox   0x900c8304  
FlushWindowObject(WindowData*, void**, unsigned char) + 672
23  com.appl