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

[Eugene Zeien]

% 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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