Dear Colm,
unfortunately, we can't read your 4D image. So could
you please put in your directory axial snapshots of 1)
the 3D template, 2) one good example among the
template_4D of one affine-registered GM image that
failed?
Thanks,
Gwenaelle
> FSLview though they
> are in sightly weird orientations the labels (A, I,
> L, etc) appear to
> be in the correct place. However, in the FAi
> versions of the subjects
> data the labels are all in the wrong places.
>
> You can see this in this image
> https://tcin.tchpc.tcd.ie/vbm/
> labels.jpg The original data is on the left and the
> FAi version is on
> the right.
>
> The generated 4D GM template is at
> https://tcin.tchpc.tcd.ie/vbm/
> template_4D_GM.nii.gz and looks quite distorted to
> my eyes.
>
> I've processed the data according to the
> instructions on the FSl
> website using this script
>
> #!/bin/sh
> echo
>
"#######################################################################
>
> #########"
> echo "### Rescaling Anatomicals"
>
> ./rescaleAnatomicals.pl
>
> # now change dir for the vbm scripts to work
> cd ../data/vbm
>
> echo
>
"#######################################################################
>
> #########"
> echo "### Skull stripping Anatomicals"
> fslvbm_1_bet -N -B
>
> echo
>
"#######################################################################
>
> #########"
> echo "### Creating template"
> fslvbm_2_template -a
>
> echo
>
"#######################################################################
>
> #########"
> echo "### Performing VBM analysis"
> fslvbm_3_proc
>
>
> The rescaleAnatomicals.pl script contains the
> following
>
==========================================================
> #!/usr/bin/perl
>
> use strict;
> use warnings;
> use Math::Libm qw(:all);
>
> sub computeScaleFactor(@);
>
> my $vbmDir = "../data/vbm/";
>
> print "Making list of anatomy files\n";
> system ("ls -1 > template_list");
>
> opendir(VBMDIR, $vbmDir) || die "Can't open $vbmDir:
> $!\n";
>
> my @anatFiles = grep { -d "$vbmDir/" && !/^\./ &&
> /\.nii.*$/ } readdir
> (VBMDIR);
>
> foreach my $anatFile ( @anatFiles ) {
> my $output = `fslstats $vbmDir/$anatFile -R`;
> my @range = split(/\s+/, $output);
> print "$anatFile: $range[0] $range[1] ";
> my $scaleFactor = computeScaleFactor(@range);
> print "$scaleFactor: ";
> my $rescaleCommand = "cd $vbmDir; tbss_1_preproc
> -f $scaleFactor
> $anatFile";
> print "Executing $rescaleCommand\n";
> system ($rescaleCommand);
> }
>
> sub computeScaleFactor(@) {
> my $scaleFactor = floor(10000 / $_[1]);
> return $scaleFactor;
> }
>
> closedir(VBMDIR);
>
> Has anybody any ideas on what as gone wrong with the
> template
> generation or is it supposed to look like that?
>
> Thanks in advance,
> --
> Dr Colm G. Connolly
> School of Psychology and Institute of Neuroscience
> The Lloyd Building
> University of Dublin
> Trinity College, Dublin 2, Éire
> Tel: +353-1-896-8475
> Fax: +353-1-671-3183
>
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