Dear John,
When I renamed the files to .palette with my Windows caret version, it
did not work. I can try this with the linux platform later today.
Jill
>>> [EMAIL PROTECTED] 03/01/05 1:00 PM >>>
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Today's Topics:
1. Displaying histological sections in Caret (Edward Craft)
2. Re: Displaying histological sections in Caret
([EMAIL PROTECTED])
3. Palette files (Jill Dorflinger)
4. Re: Displaying histological sections in Caret (John Harwell)
5. Re: Palette files (John Harwell)
----------------------------------------------------------------------
Message: 1
Date: Mon, 28 Feb 2005 21:09:12 -0500
From: "Edward Craft" <[EMAIL PROTECTED]>
Subject: [caret-users] Displaying histological sections in Caret
To: <caret-users@brainvis.wustl.edu>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I would like to generate a 3D reconstruction of macaque visual cortex
from
histological sections, onto which I can project electrophysiological
data.
Your tutorials were very helpful for getting started with Caret (thank
you!), but I've encountered a difficulty with my slice images.
The images were given to me in a CorelDraw file, in which a fine-lined
measurement grid has been superimposed on each slice. I exported the
individual slices to 1561x1219pixel tiff files, each of which covers an
area
of 25x20mm with a resolution of 150x150dpi. When I load the tiff files
into
Caret, they are displayed at a lower resolution (even when the display
window is maximized), causing some of the grid lines to fade or
disappear,
and making it difficult to see features of the smaller slices for
tracing.
Zooming using the middle mouse button in "View" mode doesn't seem to
affect
the resolution of the slice images. Are there any options for adjusting
the
scale at which the images are displayed? Thanks,
-- Ed Craft
------------------------------
Message: 2
Date: Tue, 1 Mar 2005 07:32:46 -0600 (CST)
From: [EMAIL PROTECTED]
Subject: Re: [caret-users] Displaying histological sections in Caret
To: "Edward Craft " <[EMAIL PROTECTED]>, "Caret, SureFit, and SuMS
software users" <caret-users@brainvis.wustl.edu>
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain;charset=iso-8859-1
Hi Dr. Craft,
John Harwell won't be in until a little later today, but I wanted to be
sure the problem wasn't with the exported tiff images. Have you tried
viewing the exported tiff images with a viewer other than Caret (e.g.,
PhotoShop)? Which operating system are you using? Many Linux
distributions have a graphics viewing utility named "gimp"; I'm not sure
what the corresponding utility would be for MacOSX. If you have viewed
the exported tiff images in another graphics software package, and you
don't see the resolution problem in that viewer, then you have made sure
the problem doesn't lie with the tiff images themselves.
One thing worth trying is to export them in another file format (e.g.,
jpg). Try converting just one slice, and see how it looks in Caret.
Donna
> Hi,
>
> I would like to generate a 3D reconstruction of macaque visual cortex
from
> histological sections, onto which I can project electrophysiological
data.
> Your tutorials were very helpful for getting started with Caret (thank
> you!), but I've encountered a difficulty with my slice images.
>
> The images were given to me in a CorelDraw file, in which a fine-lined
> measurement grid has been superimposed on each slice. I exported the
> individual slices to 1561x1219pixel tiff files, each of which covers
an
> area
> of 25x20mm with a resolution of 150x150dpi. When I load the tiff files
> into
> Caret, they are displayed at a lower resolution (even when the display
> window is maximized), causing some of the grid lines to fade or
disappear,
> and making it difficult to see features of the smaller slices for
tracing.
>
> Zooming using the middle mouse button in "View" mode doesn't seem to
> affect
> the resolution of the slice images. Are there any options for
adjusting
> the
> scale at which the images are displayed? Thanks,
>
> -- Ed Craft
>
>
> _______________________________________________
> caret-users mailing list
> caret-users@brainvis.wustl.edu
> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>
------------------------------
Message: 3
Date: Tue, 01 Mar 2005 09:15:57 -0500
From: "Jill Dorflinger" <[EMAIL PROTECTED]>
Subject: [caret-users] Palette files
To: <caret-users@brainvis.wustl.edu>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=US-ASCII
I just installed version 5.1 of caret on a linux platform. I use caret
to display group analyses from AFNI, so I make metric files of my AFNI
maps. I also use AFNI's palette (*.pal) files so that the clusters stay
the same colors across different displays.
The problem is I could not open an AFNI palette file in version 5.1.
The open file dialog looks for a *.palette file and not a *.pal file.
How can I use the palette I create in AFNI with caret? I would like the
clusters to be the same colors in my pictures from AFNI and my pictures
from caret.
Thanks,
Jill Dorflinger
------------------------------
Message: 4
Date: Tue, 1 Mar 2005 09:47:37 -0600
From: John Harwell <[EMAIL PROTECTED]>
Subject: Re: [caret-users] Displaying histological sections in Caret
To: "Caret, SureFit, and SuMS software users"
<caret-users@brainvis.wustl.edu>, Edward Craft
<[EMAIL PROTECTED]>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=US-ASCII; format=flowed
Hello Ed,
Caret will try to fit the entire image into to the Caret main window.
Zooming does not affect the image. You will probably need to export
your slices into a lower resolution image file, perhaps 800 x 600.
----------------------------------------------------------
John Harwell
[EMAIL PROTECTED]
314-362-3467
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave. Box 8108
St. Louis, MO 63110 USA
On Feb 28, 2005, at 8:09 PM, Edward Craft wrote:
> Hi,
>
> I would like to generate a 3D reconstruction of macaque visual cortex
> from
> histological sections, onto which I can project electrophysiological
> data.
> Your tutorials were very helpful for getting started with Caret (thank
> you!), but I've encountered a difficulty with my slice images.
>
> The images were given to me in a CorelDraw file, in which a fine-lined
> measurement grid has been superimposed on each slice. I exported the
> individual slices to 1561x1219pixel tiff files, each of which covers
> an area
> of 25x20mm with a resolution of 150x150dpi. When I load the tiff files
> into
> Caret, they are displayed at a lower resolution (even when the display
> window is maximized), causing some of the grid lines to fade or
> disappear,
> and making it difficult to see features of the smaller slices for
> tracing.
>
> Zooming using the middle mouse button in "View" mode doesn't seem to
> affect
> the resolution of the slice images. Are there any options for
> adjusting the
> scale at which the images are displayed? Thanks,
>
> -- Ed Craft
>
>
> _______________________________________________
> caret-users mailing list
> caret-users@brainvis.wustl.edu
> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>
------------------------------
Message: 5
Date: Tue, 1 Mar 2005 09:58:00 -0600
From: John Harwell <[EMAIL PROTECTED]>
Subject: Re: [caret-users] Palette files
To: "Caret, SureFit, and SuMS software users"
<caret-users@brainvis.wustl.edu>
Message-ID: <[EMAIL PROTECTED]>
Content-Type: text/plain; charset=US-ASCII; format=flowed
Hi Jill,
If you rename the *.pal file to a *.palette file will Caret read it?
If not, send the palette file directly to me so that I can determine
why Caret will not read it. I will then make a newer version of Caret5
available to you.
----------------------------------------------------------
John Harwell
[EMAIL PROTECTED]
314-362-3467
Department of Anatomy and Neurobiology
Washington University School of Medicine
660 S. Euclid Ave. Box 8108
St. Louis, MO 63110 USA
On Mar 1, 2005, at 8:15 AM, Jill Dorflinger wrote:
> I just installed version 5.1 of caret on a linux platform. I use
caret
> to display group analyses from AFNI, so I make metric files of my AFNI
> maps. I also use AFNI's palette (*.pal) files so that the clusters
> stay
> the same colors across different displays.
> The problem is I could not open an AFNI palette file in version 5.1.
> The open file dialog looks for a *.palette file and not a *.pal file.
> How can I use the palette I create in AFNI with caret? I would like
> the
> clusters to be the same colors in my pictures from AFNI and my
pictures
> from caret.
>
> Thanks,
> Jill Dorflinger
> _______________________________________________
> caret-users mailing list
> caret-users@brainvis.wustl.edu
> http://pulvinar.wustl.edu/mailman/listinfo/caret-users
>
------------------------------
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