Hello freesurfer team I have binary lesions mask from T2star images (resolution 0.3*0.3*1) already registered on freesurfer space that I would like to resample on diffusion images (that have been processed with tracula) to further exclude the lesion voxels on the DTI maps. To do so I have found several possibilities on the mailing list but I am not sure about which one is appropriate. I have tried: mri_convert but I am not sure about which resampling method to use. The nearest voxel miss quite a few lesions. I have also seen the command mri_vol2vol: mri_vol2vol --mov /subject/dmri/lowb.nii.gz --targ lesion_mask.nii.gz --inv --interp nearest --o lesion_mask_resampled.nii.gz --reg /dmri/xfms/? --no-save-reg I don't know what registration file to use in that case?
I have also seen mri_label2vol command where I could set the fill threshold parameter but I am not sure again about the registration file to use.
And eventually I also saw this command: mri_mask but I guess that the mask volume needs to be in the same dimension than the diffusion space?
Thanks a lot in advance for your help Best Celine
Hi Celine - If the lesion mask is already in the space of the freesurfer recon, you can pass to mri_vol2vol the dmri/xfms/anatorig2diff.bbr.dat transform. That's the one generated by bbregister for the anatomical-diffusion registration.
Hope this helps, a.y
On Thu, 13 Feb 2014, Celine Louapre wrote:
Hello freesurfer team I have binary lesions mask from T2star images (resolution 0.3*0.3*1) already registered on freesurfer space that I would like to resample on diffusion images (that have been processed with tracula) to further exclude the lesion voxels on the DTI maps. To do so I have found several possibilities on the mailing list but I am not sure about which one is appropriate. I have tried: mri_convert but I am not sure about which resampling method to use. The nearest voxel miss quite a few lesions. I have also seen the command mri_vol2vol: mri_vol2vol --mov /subject/dmri/lowb.nii.gz --targ lesion_mask.nii.gz --inv --interp nearest --o lesion_mask_resampled.nii.gz --reg /dmri/xfms/? --no-save-reg I don't know what registration file to use in that case?
I have also seen mri_label2vol command where I could set the fill threshold parameter but I am not sure again about the registration file to use.
And eventually I also saw this command: mri_mask but I guess that the mask volume needs to be in the same dimension than the diffusion space?
Thanks a lot in advance for your help Best Celine _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Anastasia Thanks for your answer. I think I am missing something because I tried with this registration file but the result does not look correct. I have the lesion mask in the freesurfer space that I can overlay on brainmask or dtifit_FA.nii on freeview and it seemed correctly registered on both. the command I am running is: mri_vol2vol --mov recons_dir/subj1/dmri/lowb.nii.gz --targ lesion_mask/subj1/lesion_WM.nii.gz --interp nearest --o /lesion_mask/subj1/lesion_WM_vol2vol.nii.gz --reg recons_dir/subj1/dmri/xfms/anatorig2diff.bbr.dat --no-save-reg --inv
And then when I open lesion_WM_vol2vol.nii.gz in freeview, the voxel sieze is the same as the DTI images, but the lesions are not at the same place. That is why I thought I had picked the wrong registration file...? Celine
Hi Celine - If the lesion mask is already in the space of the freesurfer recon, you can pass to mri_vol2vol the dmri/xfms/anatorig2diff.bbr.dat transform. That's the one generated by bbregister for the anatomical-diffusion registration.
Hope this helps, a.y
On Thu, 13 Feb 2014, Celine Louapre wrote:
Hello freesurfer team I have binary lesions mask from T2star images (resolution 0.3*0.3*1) already registered on freesurfer space that I would like to resample on diffusion images (that have been processed with tracula) to further exclude the lesion voxels on the DTI maps. To do so I have found several possibilities on the mailing list but I am not sure about which one is appropriate. I have tried: mri_convert but I am not sure about which resampling method to use. The nearest voxel miss quite a few lesions. I have also seen the command mri_vol2vol: mri_vol2vol --mov /subject/dmri/lowb.nii.gz --targ lesion_mask.nii.gz --inv --interp nearest --o lesion_mask_resampled.nii.gz --reg /dmri/xfms/? --no-save-reg I don't know what registration file to use in that case?
I have also seen mri_label2vol command where I could set the fill threshold parameter but I am not sure again about the registration file to use.
And eventually I also saw this command: mri_mask but I guess that the mask volume needs to be in the same dimension than the diffusion space?
Thanks a lot in advance for your help Best Celine _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Anastasia Yendiki -
Celine Louapre