Re: [Freesurfer] Apply transformation
*Od:* freesurfer-boun...@nmr.mgh.harvard.edu za uživatele Adam Rytina *Odesláno:* sobota 15. února 2020 19:52 *Komu:* Freesurfer support list *Předmět:* Re: [Freesurfer] Apply transformation External Email - Use Caution Thanks, unfortunately, I am making some mistake but I don´t know where. First of all I run autorecon1 on my anatomical T1 data (the orig.mgz image is saved in /usr/local/freesurfer/subjects/anatomical). Then in the /usr/local/freesurfer/data I run mri_robust register command of the T1 and diffusion DWI data. The registration.lta file is saved here. Don't use robust register for this, use bbregister (but you will have to run recon-all to completion) Now I add an anatomical mask "3D_T1_brain_mask.nii" to the same folder /usr/local/freesurfer/data that I want to transform to the anatomical T1 space. Is this in the conformed space (ie, same as orig.mgz)? In the same /usr/local/freesurfer/data I run : "mri_vol2vol --lta registration.lta --mov 3D_T1_brain_mask.nii --o f-in-anat3.nii --s anatomical --fstarg" If you are trying to transfer it to the DTI space, then use mri_vol2vol --lta bbr.registration.lta --targ 3D_T1_brain_mask.nii --mov dti.nii --o f-in-anat3.nii --s anatomical --interp nearest To sum up, I am aiming to apply a transformation matrix on the T1 anatomical brain mask and transform it to the T1 space defined by 3D T1 image. The problem is this command transforms orig.mgz file (a skull stripped T1 image) instead of 3D_T1_brain_mask.nii. Please, do you know where I make mistake? Thanks a lot *Od:* freesurfer-boun...@nmr.mgh.harvard.edu za uživatele Douglas Greve *Odesláno:* sobota 15. února 2020 17:15 *Komu:* freesurfer@nmr.mgh.harvard.edu *Předmět:* Re: [Freesurfer] Apply transformation Yes, mri_vol2vol On 2/15/20 11:07 AM, Adam Rytina wrote: External Email - Use Caution Hello all, I want to apply the saved transformation (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) on my input anatomical mask and change a final FOV by specifying a diffusion reference image (its voxels size). It means to apply the same command as the command ApplyXFM in FSL FLIRT. Does this option exist also in Freesurfer? Thanks a lot Regards Adam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Apply transformation
External Email - Use Caution Hello all, is it possible to transform a binary mask (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) and change a final FOV by specifying a diffusion reference image? Or the transform can be applied only on structural image? I am still struggling with the transformation of my binary mask as explained below. Thanks a lot Regards Adam Od: Adam Rytina Odesláno: středa 19. února 2020 8:11 Komu: Greve, Douglas N.,Ph.D. Předmět: Fw: [Freesurfer] Apply transformation Hello, please, could you help me with this case? What am I doing wrong? Thanks a lot Od: freesurfer-boun...@nmr.mgh.harvard.edu za uživatele Adam Rytina Odesláno: sobota 15. února 2020 19:52 Komu: Freesurfer support list Předmět: Re: [Freesurfer] Apply transformation External Email - Use Caution Thanks, unfortunately, I am making some mistake but I don´t know where. First of all I run autorecon1 on my anatomical T1 data (the orig.mgz image is saved in /usr/local/freesurfer/subjects/anatomical). Then in the /usr/local/freesurfer/data I run mri_robust register command of the T1 and diffusion DWI data. The registration.lta file is saved here. Now I add an anatomical mask "3D_T1_brain_mask.nii" to the same folder /usr/local/freesurfer/data that I want to transform to the anatomical T1 space. In the same /usr/local/freesurfer/data I run : "mri_vol2vol --lta registration.lta --mov 3D_T1_brain_mask.nii --o f-in-anat3.nii --s anatomical --fstarg" To sum up, I am aiming to apply a transformation matrix on the T1 anatomical brain mask and transform it to the T1 space defined by 3D T1 image. The problem is this command transforms orig.mgz file (a skull stripped T1 image) instead of 3D_T1_brain_mask.nii. Please, do you know where I make mistake? Thanks a lot Od: freesurfer-boun...@nmr.mgh.harvard.edu za uživatele Douglas Greve Odesláno: sobota 15. února 2020 17:15 Komu: freesurfer@nmr.mgh.harvard.edu Předmět: Re: [Freesurfer] Apply transformation Yes, mri_vol2vol On 2/15/20 11:07 AM, Adam Rytina wrote: External Email - Use Caution Hello all, I want to apply the saved transformation (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) on my input anatomical mask and change a final FOV by specifying a diffusion reference image (its voxels size). It means to apply the same command as the command ApplyXFM in FSL FLIRT. Does this option exist also in Freesurfer? Thanks a lot Regards Adam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Apply transformation
External Email - Use Caution Hello, please, could you help me with this case? What am I doing wrong? Thanks a lot Od: freesurfer-boun...@nmr.mgh.harvard.edu za uživatele Adam Rytina Odesláno: sobota 15. února 2020 19:52 Komu: Freesurfer support list Předmět: Re: [Freesurfer] Apply transformation External Email - Use Caution Thanks, unfortunately, I am making some mistake but I don´t know where. First of all I run autorecon1 on my anatomical T1 data (the orig.mgz image is saved in /usr/local/freesurfer/subjects/anatomical). Then in the /usr/local/freesurfer/data I run mri_robust register command of the T1 and diffusion DWI data. The registration.lta file is saved here. Now I add an anatomical mask "3D_T1_brain_mask.nii" to the same folder /usr/local/freesurfer/data that I want to transform to the anatomical T1 space. In the same /usr/local/freesurfer/data I run : "mri_vol2vol --lta registration.lta --mov 3D_T1_brain_mask.nii --o f-in-anat3.nii --s anatomical --fstarg" To sum up, I am aiming to apply a transformation matrix on the T1 anatomical brain mask and transform it to the T1 space defined by 3D T1 image. The problem is this command transforms orig.mgz file (a skull stripped T1 image) instead of 3D_T1_brain_mask.nii. Please, do you know where I make mistake? Thanks a lot Od: freesurfer-boun...@nmr.mgh.harvard.edu za uživatele Douglas Greve Odesláno: sobota 15. února 2020 17:15 Komu: freesurfer@nmr.mgh.harvard.edu Předmět: Re: [Freesurfer] Apply transformation Yes, mri_vol2vol On 2/15/20 11:07 AM, Adam Rytina wrote: External Email - Use Caution Hello all, I want to apply the saved transformation (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) on my input anatomical mask and change a final FOV by specifying a diffusion reference image (its voxels size). It means to apply the same command as the command ApplyXFM in FSL FLIRT. Does this option exist also in Freesurfer? Thanks a lot Regards Adam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Apply transformation
External Email - Use Caution Thanks, unfortunately, I am making some mistake but I don´t know where. First of all I run autorecon1 on my anatomical T1 data (the orig.mgz image is saved in /usr/local/freesurfer/subjects/anatomical). Then in the /usr/local/freesurfer/data I run mri_robust register command of the T1 and diffusion DWI data. The registration.lta file is saved here. Now I add an anatomical mask "3D_T1_brain_mask.nii" to the same folder /usr/local/freesurfer/data that I want to transform to the anatomical T1 space. In the same /usr/local/freesurfer/data I run : "mri_vol2vol --lta registration.lta --mov 3D_T1_brain_mask.nii --o f-in-anat3.nii --s anatomical --fstarg" To sum up, I am aiming to apply a transformation matrix on the T1 anatomical brain mask and transform it to the T1 space defined by 3D T1 image. The problem is this command transforms orig.mgz file (a skull stripped T1 image) instead of 3D_T1_brain_mask.nii. Please, do you know where I make mistake? Thanks a lot Od: freesurfer-boun...@nmr.mgh.harvard.edu za uživatele Douglas Greve Odesláno: sobota 15. února 2020 17:15 Komu: freesurfer@nmr.mgh.harvard.edu Předmět: Re: [Freesurfer] Apply transformation Yes, mri_vol2vol On 2/15/20 11:07 AM, Adam Rytina wrote: External Email - Use Caution Hello all, I want to apply the saved transformation (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) on my input anatomical mask and change a final FOV by specifying a diffusion reference image (its voxels size). It means to apply the same command as the command ApplyXFM in FSL FLIRT. Does this option exist also in Freesurfer? Thanks a lot Regards Adam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Apply transformation
Yes, mri_vol2vol On 2/15/20 11:07 AM, Adam Rytina wrote: External Email - Use Caution Hello all, I want to apply the saved transformation (a transformation matrix 4x4 acquired by registration of an anatomical and a diffusion image) on my input anatomical mask and change a final FOV by specifying a diffusion reference image (its voxels size). It means to apply the same command as the command ApplyXFM in FSL FLIRT. Does this option exist also in Freesurfer? Thanks a lot Regards Adam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] apply transformation using talairach.m3z
glad to hear it worked! You can control the conversion to int by using -odt, --out_data_type cheers Bruce On Sun, 22 Oct 2017, Gidon Levakov wrote: > Hi, > > I think I got the problem, just updating, so other people won't do the same > mistake: > > The warp stored in the 'talairach.m3z' file should be applied on a conformed > volume, meaning the raw > image after the the following command was cried out: > "mri_convert img.nii.gz img_conformed.nii.gz --conform" (conform to 1mm voxel > size in coronal) > > then the warp can simply applied by the following command: > 'mri_convert img_conformed.nii.gz --apply_transform talairach.m3z -oc 0 0 0 > img_warped.nii' (works > for me!) > > I also noticed that the '--conform' option convert the img data type to > integer (if it was float > before, like in my case, where it turned all the values to 0). So you should > be aware to that. > > Good luck! > gidon l. > > > 2017-10-19 16:40 GMT+03:00 Gidon Levakov : > Hi Freesurfer experts, > > I have several nifti images (created with another software) in the subjects > original > anatomical space (native space) that I want to transform to a common space > (freesurfer version > of MNI305 should be fine) using non-linear transformation. > > Reading a previous answer regarding this issue > (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033556.html), > I > understand I should use the mri_vol2vol command to apply the transformation > stored in the file > mri/transforms/talairach.m3z (I already run recon all). But after checking > the result, the > images are still not align with each other and do not resemble the > mni305.cor.mgz file. > > I used the following command: > > mri_vol2vol --m3z my_subjects_dir/sub_X/mri/transforms/talairach.m3z > --noDefM3zPath > --reg_header --mov file_loc/img.nii.gz --targ > /usr/local/freesurfer/average/mni305.cor.mgz --o > file_loc/img_warped.nii.gz > > I also tried without the --reg_header option with no success. > > Any idea what I am doing wrong? can you give me an example that works? > > Thanks in advance! > > Gidon l. > > > > > > > > ___ 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] apply transformation using talairach.m3z
Hi, I think I got the problem, just updating, so other people won't do the same mistake: The warp stored in the 'talairach.m3z' file should be applied on a *conformed volume*, meaning the raw image after the the following command was cried out: "mri_convert img.nii.gz img_conformed.nii.gz --conform" (conform to 1mm voxel size in coronal) then the warp can simply applied by the following command: 'mri_convert img_conformed.nii.gz --apply_transform talairach.m3z -oc 0 0 0 img_warped.nii' (works for me!) I also noticed that the '--conform' option convert the img data type to integer (if it was float before, like in my case, where it turned all the values to 0). So you should be aware to that. Good luck! gidon l. 2017-10-19 16:40 GMT+03:00 Gidon Levakov : > Hi Freesurfer experts, > > I have several nifti images (created with another software) in the > subjects original anatomical space (native space) that I want to transform > to a common space (freesurfer version of MNI305 should be fine) using > non-linear transformation. > > Reading a previous answer regarding this issue ( > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/ > 2013-September/033556.html), I understand I should use the *mri_vol2vol* > command to apply the transformation stored in the file > *mri/transforms/talairach.m3z* (I already run recon all). But after > checking the result, the images are still not align with each other and do > not resemble the *mni305.cor.mgz* file. > > I used the following command: > > mri_vol2vol --m3z my_subjects_dir/sub_X/mri/transforms/talairach.m3z > --noDefM3zPath --reg_header --mov file_loc/img.nii.gz --targ > /usr/local/freesurfer/average/mni305.cor.mgz --o > file_loc/img_warped.nii.gz > > I also tried without the --reg_header option with no success. > > Any idea what I am doing wrong? can you give me an example that works? > > Thanks in advance! > > Gidon l. > > > > > > > ___ 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. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
