[Brains-users] Can't open trimodal images!

[Ronald Pierson]

The trimodal image is simply loading the three resampled images at once, 

b2 load image {T1Image T2Image PDImage}

Simply enter that command on the brains2 command line with the full or
relative paths to the images and it should load.  The T1 contributes the red
color, the T2 contributes the green, and the PD is the blue.  This has been
helpful for some basal ganglia tracing in the past - see some of the tracing
guidelines on our web site.  Makes my eyes hurt though....

Trimodal enhanced and trimodal class images are other sets of images that
have to be generated by other routines.  I am not sure the steps to generate
those images are documented in the user guide, and we haven't used them for
anything but the most obnoxious tracing projects.  I am pretty certain that
the trimodal class images are no longer available at all, but they were kind
of neat.  I believe they were built from discriminant images, which were
simply images that represented how WM, CSF & blood were discriminated from
gray matter.  Here is a link to a snapshot of one I had from a few years
ago.

www.psychiatry.uiowa.edu/users/ronald/mr6discrim1.jpg


ron



-----Original Message-----
From: brains-users-bounces at psychiatry.uiowa.edu
[mailto:brains-users-bounces at psychiatry.uiowa.edu] On Behalf Of Eugene Zeien
Sent: Friday, February 17, 2006 3:44 PM
To: Lee, Buyean
Cc: 'brains-users at psychiatry.uiowa.edu'; 'Andrew Bokarius'
Subject: Re: [Brains-users] Can't open trimodal images!

% grep -l trimodal /opt/brains2/bin/scripts/iplTclScripts/*.tcl
/opt/brains2/bin/scripts/iplTclScripts//b2IPLutils.tcl
% nedit /opt/brains2/bin/scripts/iplTclScripts//b2IPLutils.tcl &
## Ah, ha!  This routine is trying to use 'getACPCdir' to find the
## relevant ACPC directory.
% grep -l getACPCdir /opt/brains2/bin/scripts/iplTclScripts/*.tcl
## Several matches, will skip listing all of them. utils.tcl is
## prime suspect  ;-)
% nedit /opt/brains2/bin/scripts/iplTclScripts//b2IPLutils.tcl &
set index [string first "_ACPC" $pathName]
## So, BRAINS is looking at the current directory $pathName and
## trying to find a substring "_ACPC".
## Failure to find this substring would produce the error,
## "failed to obtain current ACPC directory"

## As for the trimodal images themselves, it appears the .tcl
## script is looking specificly for
     if {[file exists $myPath/${scanId}_grey_blood.hdr] == 1} {
     if {[file exists $myPath/${scanId}_grey_white.hdr] == 1} {
     if {[file exists $myPath/${scanId}_grey_csf.hdr] == 1} {
## i.e. the user has no options regarding filenaming.
## The filenames must match the above templates.

Lee, Buyean wrote:
> Dear other Brains2 users,
> 
>  
> 
> Currently we use Medx to draw ROIs on MRI to create three-dimensional mask
> for PET image analysis, but we find that Brains2 seems to be a better
image
> processing software for this purpose.
> 
>  
> 
> Therefore, we have installed Brains2 in our RedHat Linux computer.
> 
> It seemed to work as it supposed to do.
> 
> But, we are having difficulty in following the PDF instruction manual to
> enhance image with trimodal images.
> 
> I would like to ask help from other Brains2 users.
> 
>  
> 
> We can open and play with T1, T2, and PD MRI files separately, but we were
> unable to load the trimodal images. 
> 
> The error message that appears is 
> 
> 
> 
> "some or all of the resampled images do not exist"
> 
> 
> 
> and when we try to load trimodal-class, the error is: 
> 
> 
> 
> "failed to obtain current ACPC directory" and 
> "some or all of the discriminant images do not exist". 
> 
> 
> 
> Please let us know what we should consider doing in order to be able to
load
> trimodal images.
> 
>  
> 
> Thank you,
> 
>  
> 
> Buyean
> 
>  
> 
> 
> 
> 
> ------------------------------------------------------------------------
> 
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> Brains-users mailing list
> Brains-users at www.psychiatry.uiowa.edu
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