Posted by
Jonathan Jackson-2 on
Feb 25, 2008; 2:04pm
URL: http://imagej.273.s1.nabble.com/Re-Nifti-conversion-tp3697090.html
On Mon, 18 Feb 2008 16:18:06 -0500, Rajagopalan, Venkateswaran
<
[hidden email]> wrote:
>Dear All,
>
>It will be of great help to me if you could clarify the following;
>
>1) I am using Image J to convert my dicom images to NIFTI format. When i
load the nifti formatted images into FSL (to do image registration) these
images appear inverted, i also tried the rotate option before saving them
into NIFTI format but it doesn't work.
>
What happens if you save as Analyze 7.5 instead of NIFTI? NIFTI images are
different to the older Analyze 7.5 in that they store information about the
image orientation. ImageJ does not take this into account when displaying
the image, but FSL does. Both programs should display the same though, if
you use Analyze format. There are some tools included with FSL that allow
viewing / editing of the orientational information, eg. 'fslhd' and
'fslorient'.
>2) While doing T2 calculation using MRI T2 calculations option (using dicom
images) 16 bit i am not able to see different structures within the brain
clearly whereas if i convert my dicom images to 8 bit then i am able to see
all the structures within the brain in my t2 maps.
Try converting to 'float' before doing the calculation, and converting back
to 16 bit signed (I'm assuming your data are signed) afterwards with a
plugin found here:
http://rsb.info.nih.gov/ij/plugins/converter.html.
regards,
Jon