[Mristudio-users] question on getting to byte data format for LDDMM

[susumu]

1: For LDDMM, definitely the single-subject. LDDMM aggressively identifies
and matches structures. The population-averaged maps have very blur
structural definitions, which confuses LDDMM. For linear and low-order
non-linear, the population averaged is better because it maximizes the
matching between the normalized subject and atlas after such low-level
transformations.

2: Yes, all images have to be converted to byte. This can be easily done by
the "BWF" button in the top section. Please note that once the images such
as FA is converted to byte, it is usable to drive LDDMM, but not usable for
the subsequent quantification (who wants FA values 0 - 255?). So, you have
to apply the resultant transformation matrix to FA later. 

Related to this issue, we are testing ADC (trace) not b0 image to drive
LDDMM (I mean FA + ADC dual channel). The reason is, FA and ADC maps are
quantitative maps and do not require histogram (intensity) matching. When
you convert FA&ADC to byte, you can specify the absolute range for the
conversion (for example, byte 0 = FA 0 or ADC 0 / byte 255 = FA 1 or ADC 3.5
(trace 10)). The latest version can specify the absolute range conversion.
This makes our life easier. Because LDDMM operates on intensity, intensity
matching is important. Our single subject atlas is from Philips which has a
certain degree of intensity distribution, which is different from Siemens.
Without intensity matching, LDDMM won't work.

-----Original Message-----
From: mristudio-users-bounces at mristudio.org
[mailto:mristudio-users-bounces at mristudio.org] On Behalf Of Elizabeth Finger
Sent: Thursday, July 31, 2008 5:04 PM
To: dti studio help
Subject: [Mristudio-users] question on getting to byte data format for LDDMM


Hello-

I am at the step of sending an individual subject's data to LDDMM for
automatic tract segementation, and have run into the following questions:

1. For single subjects, do you recommend normalizing to the ICBM group atlas
or to the JHU-MNI single subject atlas?

2. After loading the template B0 and FA images, and then our subject mean
B0, FA, DWI, eigenvalue and tensor, we did the AIR linear transformation in
Landmarker using the template B0 and the subject B0 images.  We then saved
each 'updated files'  files (and the tensors together)in the raw image
format following the normalization.  When I then attempt to use histogram
buttons or the the single channel LDDMM button, an error pops up that says
the subject data must be in byte format.  Clicking on the multple channel
LDDMM, we can see the input screen, but once we load up the template BO and
FA and the subject B) and FA and try to submit, we get the same error
message that the subject data must be in byte format.  We are not sure how
to convert the updated-normalized images from Landmarker to byte format for
LDDMM?

Thank you,

Elizabeth Finger

 
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