Re: [Freesurfer] dt_recon and mri_vol2vol issue
Did you check the registration? My guess is that the registration failed
because the initial FSL registration failed. I've put a new version here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/dt_recon
it has a better initializer. Just copy it over the one in
$FREESURFER_HOME/bin (make a backup of the original one though)
On 2/25/19 1:50 PM, Daniel Callow wrote:
>
> External Email - Use Caution
>
> Hello freesurfer experts,
>
> I am running dt_recon with the following script
>
> dt_recon --sd /Volumes/DANIEL/dti_freesurf/diffusion_recons --i
> /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/image01.dcm
> --s ${subj}.${cond} --b dwi.bvals dwi.voxel_space.bvecs --o
> /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}.
>
>
> and mri_vol2vol to get the wmparc and aseg.mgz files in my lowb space
> with the script below
>
> mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz
> --targ $subj_dir/diffusion_recons/${subj}.${cond}/mri/wmparc.mgz --inv
> --interp nearest --o
> /Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/wmparc2diff.mgz
>
> --reg $subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg
>
>
> mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz
> --targ $subj_dir/diffusion_recons/${subj}.${cond}/mri/aseg.mgz --inv
> --interp nearest --o
> $subj_dir/dtrecon/${subj}.${cond}./aseg2diff.nii.gz --reg
> $subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg
>
>
> However, one of my subjects shows a major issue with the mri_vol2vol
> registration (for most of the subject scans it seems to work no
> problem). When looking at the wmparc2diff.mgz I created (screenshot
> attached), it is apparent that the registration of the wmparc to
> wmparc2diff space actually causes wmparc2diff.mgz to be further from
> the lowb than wmparc is. This same registration issue occurs for aseg.mgz.
>
>
> I assume this means there is an issue with the register.dat file for
> this subject? If so is there any way to troubleshoot the issue and get
> a correct register.dat file?
>
>
> For reference, the following commands and registration steps have
> worked for other subjects, as well as this same subject's scans under
> another condition.
>
>
> Any advice with troubleshooting would be greatly appreciated.
>
>
> Best,
>
> *Daniel Callow*
> /PhD Student, Neuroscience and Cognitive Science/
> Exercise for Brain Health Lab
> University of Maryland, College Park
> _ddcc2...@gmail.com _
> 443-254-6298
>
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[Freesurfer] dt_recon and mri_vol2vol issue
External Email - Use Caution
Hello freesurfer experts,
I am running dt_recon with the following script
dt_recon --sd /Volumes/DANIEL/dti_freesurf/diffusion_recons --i
/Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/image01.dcm
--s ${subj}.${cond} --b dwi.bvals dwi.voxel_space.bvecs --o
/Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}.
and mri_vol2vol to get the wmparc and aseg.mgz files in my lowb space with
the script below
mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ
$subj_dir/diffusion_recons/${subj}.${cond}/mri/wmparc.mgz --inv --interp
nearest --o
/Volumes/DANIEL/dti_freesurf/diffusion_recons/${subj}.${cond}/mri/wmparc2diff.mgz
--reg $subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg
mri_vol2vol --mov $subj_dir/dtrecon/${subj}.${cond}./lowb.nii.gz --targ
$subj_dir/diffusion_recons/${subj}.${cond}/mri/aseg.mgz --inv --interp
nearest --o $subj_dir/dtrecon/${subj}.${cond}./aseg2diff.nii.gz --reg
$subj_dir/dtrecon/${subj}.${cond}./register.dat --no-save-reg
However, one of my subjects shows a major issue with the mri_vol2vol
registration (for most of the subject scans it seems to work no problem).
When looking at the wmparc2diff.mgz I created, it is apparent that the
registration of the wmparc to wmparc2diff space actually causes
wmparc2diff.mgz to be further from the lowb than wmparc is (the brain is
shifted severely to the right). This same registration issue occurs for
aseg.mgz.
When I look at fa-tal.nii.gz it is poorly registered (again worse than FA
overlayed on aseg or wmparc which happens to be pretty close without
dt_recon). I assume this means there is an issue with the register.dat file
for this subject? If so is there any way to troubleshoot the issue and get
a correct register.dat file from dt_recon?
For reference, the following commands and registration steps have worked
for other subjects, as well as this same subject's scans under a different
condition. At first glance there don't seem to be any specific issues with
the anatomical or diffusion images before the registration attempt.
Any advice with troubleshooting would be greatly appreciated.
Best,
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
*Daniel Callow*
*PhD Student, Neuroscience and Cognitive Science*
Exercise for Brain Health Lab
University of Maryland, College Park
*ddcc2...@gmail.com *
443-254-6298
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