[MINC-users] classify_clean

[Jason Lerch]

On Apr 6, 2005, at 1:37 PM, roberto wrote:

> Hi there! (this is my first e-mail to the list... )

Welcome!

>
> 1. how does classify_clean work with multiple input volumes? (a t1, t2 
> and pd)
> it would be nice if there was an example of it in the wiki...

Theoretically? Your best bet is taking a look at

Zijdenbos, A. P., Forghani, R. and Evans, A. C. (2002) Automatic 
"pipeline" analysis of 3-D MRI data for clinical trials: application to 
multiple sclerosis. IEEE Trans Med Imaging 21, 1280-1291.

If you mean practically, then simply append them to the command line, 
i.e.

classify_clean -clean_tags t1.mnc t2.mnc pd.mnc output_classified.mnc

>
> 2. also, I'm having problems running nu_correct (v1.10) with some 
> volumes (which appear to have long headers). Any idea?

N3's header handling has always been rather dumb - so unless someone 
fixed that recently, you probably have to remove the dicom part of the 
header. Create a script like the following

#!/usr/local/bin/perl5 -w

open IN, "$ARGV[0]";
open OUT, ">/tmp/mincedittmp_$$.txt";

while (<IN>) {
     if ($_ =~ /dicom_0x.+/) {
         # do nothing
     }
     else {
         print OUT $_;
     }
}

close IN;
close OUT;

system("mv /tmp/mincedittmp_$$.txt $ARGV[0]");


and run 'mincedit mincfile.mnc above_script.pl' before running N3. You 
might of course have to adapt that script to your needs.

Jason

>
> thanks!
> roberto
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