 |
 |
Yes. For step 5, you can actually specify
the two warpfields in probtrackx as --xfm=MNI2diff --invxfm=diff2MNI instead of
explicitly transforming the ROIs.
Peace,
Matt.
From:
Sent: Saturday, November 20, 2010
1:28 AM
To: [log in to unmask]
Subject: Re: [FSL] problems with
Partial FOV Registration
Thank you for your help.
if I want to do probtracking and need to register some ROIs in
MNI space, such as AAL templates, to individual space, which will be used
as seed masks and targets masks, We also should do my registrations by
individual FA images like you said. Am I right?
On Sat, Nov 20, 2010 at 5:22 AM, Matt Glasser <[log in to unmask]> wrote:
I would do your registrations in the following way:
1) Distortion correct your diffusion data
2) Register FA to individual T1 using –dof 6 (if you don’t distortion
correct, you might use –dof 12, but the registration will not be exact because
distortions are nonlinear)
3) Register individual T1 to MNI152 using FLIRT and FNIRT
4) Convertwarp to concantinate all transforms, and invwarp to invert
the warp
5) Use the inverted warpfield to map data from MNI to your individual
subject’s diffusion space.
I wouldn’t worry about only a few slices lacking, as long as the
registration works. I would not use the b0 for registration, as its
contrast is more different than the FA. I don’t know why people started
doing that.
Peace,
Matt.
From:
Sent: Friday, November 19, 2010
7:34 AM
To: [log in to unmask]
Subject: [FSL] problems with
Partial FOV Registration
Hi
I have some rest and DTI data with few slices on the top lack。I
just read the suggestions on the websit, which recommeds to use the xyztrans.sch and less
DOF. My problem is about the fnirt part of registration from 3D to MNI. How can
I registrate the individial funcitonal space with small FOV to MNI space.
And
are these following steps right？
1.registrate
the partial_brain to high resolution 3D with xyztrans.sch and less DOF.
2.registrate
the 3D to MNI using flirt and fnirt with normal methods, get the mat and warp
field
3. convertwarp
all the mat and warp together, get the one partial_brain_to_MNI_warped.nii.gz,
and invertwarp it and get the MNI_to_partial_brain_warped.nii.gz
4.
apply these coefficient images to individual images.
usually I learned to use the b0 image in DTI for registration. Sometimes I read
some papers which said register individual_FA to MNI. I am confused the
differences between them.
if I want to registrate JHU-ICBM-tracts-prob-2mm.nii.gz to individual diffusion
space, what should I do? I read some paper in which researchers used the
individual_FA image as a reference. But I really was puzzled by the reasons.
And what should I do If the individudal_FA iamges are with few slices lack in
the top.
maybe these questions are so stupid. But as a green hand, I just want to
make sure I do not make mistakes about the data processing and really know how
and why to do that.
any help will be appreciated
--
Xuemei Lei
National Key Laboratory of Cognitive Neuroscience and Learning
Tel: +86-13269171259
Email: [log in to unmask]
Blog: www.dubo.in
Web: http://psychbrain.bnu.edu.cn
==============================================
Welcome to the Blog: www.dubo.in
--
Xuemei Lei
National Key Laboratory
of Cognitive Neuroscience and Learning
Tel: +86-13269171259
==============================================
Welcome to visit my blog: www.mobiye.com