The answer is in the help, I think: dt_recon --help
doug
Kjell Inge wrote:
I am using Freesurfer and I am having difficulties in coregistration of a DTI volume to the anatomy image. I have been running
recon-all -i <anatomy1.nii> -i <anatomy2.nii> -s 2005_anatomy
followed by
recon-all -autorecon1 -s 2005_anatomy
and then
dt_recon --i dti/subj_539_dti.nii --b dti/aging_hds_2005_dti.bval dti/aging_hds_2005_dti.bvec --s 2005_anatomy --o outputdti
where "dti/subj_539_dti.nii" is my DTI volume, "aging_hds_2005_dti.bval" and "dti/aging_hds_2005_dti.bvec" are my bval and bvec files and "2005_anatomy" is my subject folder. I have made an output folder inside "2005_anatomy" named "outputdti" My bval and bvec files are attached below.
Everything runs smoothly with no error messages, and there is a bunch of files created in "outputdti". Now, my questions are as follow:
- How do I see the registered DTI (for instance the FA) visualized on
the anatomy? Is the finally registered FA image inside the file "FA.nii" or do you have to run a transformation on that? If so, which transformation and how is that done? There are several files containing rigid transformations, the .reg files and the register.dat file.
When I check FA.nii it does NOT seem to be coregistered with my anatomical input image. What went wrong?
- When I open the image "mask.nii" it is like a white box, no
structures, is this really correct? Does this mean that the BET has not succeeded? However, when I open "brainmask.mgz" by "tkmedit" it is certainly skullstripped.
- Does dt_recon really do a nonlinear registration? When looking
through the script, I can only see that dt_recon uses flirt (inside "eddy_correct" on the "dwi.nii", producing "dwi-ec.nii" and inside "fslregister", applied to "lowb.nii") which is an affine registration tool.
I hope someone can solve my problems.
Erlend
bvec: 0 0 0 0 0 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000 1000
bval: 0 0 0 0 0 -0.532213 -0.25014 0.633507 0.218922 0.41315 -0.734236 -0.93647 0.333112 -0.103315 0.92654 -0.801489 0.916837 0.537756 0.213559 0.124139 -0.27398 0.443315 -0.024171 -0.568365 -0.93093 0.825459 -0.472598 -0.504263 -0.149336 0.694717 0 0 0 0 0 0.104013 -0.721834 -0.753136 0.850393 -0.780294 -0.661804 0.054189 -0.242859 -0.991677 0.372983 0.543143 -0.261948 0.438028 -0.664684 -0.051816 0.960273 0.878048 0.368772 0.637098 -0.168158 -0.182178 -0.629557 -0.129265 0.688743 0.344412 0 0 0 0 0 -0.840197 0.64528 -0.177358 0.478441 0.469519 0.151371 0.346537 0.911074 -0.076828 -0.04907 -0.250221 0.30132 -0.720382 -0.715952 -0.990911 -0.053015 -0.180284 0.929206 0.520641 -0.324178 -0.534255 -0.616692 0.85382 -0.709459 0.631465
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