Hi all > > When you loaded the lowb into freeview and it looked registered with the > anatomical, did you load the lowb with the registration file? If not, > then the registration may be wrong. Things may look almost right when > you don't specify a registration file because you probably collected the > dti and anatomical in the same session. If so, then check the > registration with something like > > tkregister2 --mov lowb.nii.gz --reg anatorig2diff.bbr.dat --surfs
I did not load it with the registration file, but I just did and it does not change the results on freeview. I also checked the registration on tkregister and it seems very fine to me. > > also, what is the first value in anatorig2diff.bbr.dat.mincost? Here are all the values: 0.180949 209.653007 285.934948 29.944402 Maybe one point that I don't understand is why we have to apply a registration matrix if all the volumes (brainmask.mgz, lowb.nii.gz and the lesion mask) are already registered? Because if I am applying the invert of registration matrix anatorig2diff.bbr.dat to the lesion mask, then it will be in the native diffusion space, not the recons space anymore, isn't it? > > > > doug > > > > > > On 2/17/14 10:41 PM, Celine Louapre wrote: >> The lesion_vol2vol volume is still not correctly overlapping the DTI. >> >> The only command that didn't give me registration issue is mri_convert >> where I did not put any registration file but I was not completely happy >> with the interpolation resampling. (nearest missed some lesions, maybe >> interpolate and then binarize the mask was one possible option). I can >> show you the results tomorrow if you prefer >> Celine >> >>> what does it look like if you run >>> >>> tkmedit -f lowb.nii.gz -ov lesion_WM_vol2vol.nii.gz -fminmax .5 1 >>> >>> >>> >>> On 2/17/14 10:00 PM, Celine Louapre wrote: >>>> No problem, sorry! >>>> So when I am loading my lesion mask on freeview on brainmask.mgz and >>>> on >>>> DTI_fit_FA.nii, the lesions are correctly registered on both DTI and >>>> T1. >>>> The only thing I would like to do is to resample the lesion mask that >>>> has >>>> a resolution of 0.3*0.3*1 on the resolution of the DTI that has >>>> 1.8mm^3. >>>> When I am using the command below with mri_vol2vol, and the >>>> registration >>>> matrix anatorig2diff.bbr.dat, the output is a lesion mask that has >>>> 1.8mm3 >>>> resolution, but the lesions are not overlapping the other modalities >>>> and >>>> the previous mask on freeview. Is it the way I am loading it on >>>> freeview >>>> maybe? or actually all the volumes are already on the recons space so >>>> maybe I should not use any registration matrix? >>>> Celine >>>> >>>>> oops, sorry! That command looks like it is correct. Can you say more >>>>> about what is going wrong? How are you determining that something is >>>>> going wrong? >>>>> doug >>>>> >>>>> >>>>> >>>>> >>>>> On 2/17/14 9:30 PM, Celine Louapre wrote: >>>>>> Hi Doug >>>>>> I don't know if you had the chance to read my email below to >>>>>> resample >>>>>> a >>>>>> lesion mask on diffusion images. Anastasia gave me the registration >>>>>> file >>>>>> to use (anatorig2diff.bbr.dat) in the command but the output mask >>>>>> file >>>>>> was >>>>>> not registered anymore. So she asked me to rephrase my question more >>>>>> generally on the mailing list to look for help with bbregister. >>>>>> Thanks a lot >>>>>> Celine >>>>>> >>>>>> >>>>>> ---------------------------- Original Message >>>>>> ---------------------------- >>>>>> Subject: [Freesurfer] Resample a mask on diffusion images using >>>>>> bbregister >>>>>> registration matrix >>>>>> From: "Celine Louapre" <cel...@nmr.mgh.harvard.edu> >>>>>> Date: Thu, February 13, 2014 9:58 pm >>>>>> To: freesurfer@nmr.mgh.harvard.edu >>>>>> -------------------------------------------------------------------------- >>>>>> >>>>>> 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 to further exclude the lesion voxels on the DTI >>>>>> maps >>>>>> (and >>>>>> to calculate DTI metrics within the lesions too). >>>>>> Using mri_vol2vol command I think I am missing something because I >>>>>> tried >>>>>> with the registration file produced by bbregister (through tracula) >>>>>> 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 seems 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 >>>>>> size >>>>>> is the same as the DTI images, but the lesions are not at the same >>>>>> place. >>>>>> >>>>>> On the mailing list I have also seen other options but I am not sure >>>>>> if >>>>>> they would be appropriate? >>>>>> I have seen mri_label2vol command where I could set the fill >>>>>> threshold >>>>>> parameter but it does not solve the problem of the registration >>>>>> file? >>>>>> also mri_convert >>>>>> And eventually I also saw this command: >>>>>> mri_mask but I guess that the mask volume needs to be in the same >>>>>> dimension as the diffusion space? >>>>>> >>>>>> Thanks a lot >>>>>> Best >>>>>> Celine >>>>>> >>>>>> >>>>>> >>>>> >>> >>> >> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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