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Thank you very much! On Sun, Nov 21, 2010 at 12:39 AM, Matt Glasser <[log in to unmask]> wrote: > 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:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On > Behalf Of *xuemei lei > *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:* FSL - FMRIB's Software Library [mailto:[log in to unmask]] *On > Behalf Of *xuemei lei > *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 > Beijing Normal University > Beijing, China. 100875 > 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<http://psychbrain.bnu.edu.cn> > Beijing Normal University > Beijing, China. 100875 > Tel: +86-13269171259 > ============================================== > Welcome to visit my blog: www.mobiye.com > -- Xuemei Lei National Key Laboratory of Cognitive Neuroscience and Learning<http://psychbrain.bnu.edu.cn> Beijing Normal University Beijing, China. 100875 Tel: +86-13269171259 ============================================== Welcome to visit my blog: www.mobiye.com