Hi Anastasia and freesurfer experts I am having some troubles with the registration of DTI images processed with tracula for one subject. When I load the lowb.nii.gz on freeview together with brainmask, it is not registered, but when I am loading it with the registration matrix anatorig2diff.bbr.dat, it is correctly registered. I don't have to specify the registration file for the other subjects, is that an issue of this particular subject? I am concerned because we later sampled surfaces on the DTI images, so I guess if the surf from the recon space is not correctly displayed on the DTI images, then my sampling is probably wrong too? The tracts are correctly displayed on the native DTI images, but if I want to display them on the anat space then it is not correct. Thanks for your help Celine
In general you should use a registration file when viewing your results. In many cases, it may look like it is in registration with out a registration file. This can happen if you acquired your anatomical and DTI data in the same session. For this subject, were they acquired in different sessions or was the subject removed and replaced back in the scanner? When you sample the data onto the surfaces, you should always use a registration file.
doug
On 02/27/2014 05:08 PM, Celine Louapre wrote:
Hi Anastasia and freesurfer experts I am having some troubles with the registration of DTI images processed with tracula for one subject. When I load the lowb.nii.gz on freeview together with brainmask, it is not registered, but when I am loading it with the registration matrix anatorig2diff.bbr.dat, it is correctly registered. I don't have to specify the registration file for the other subjects, is that an issue of this particular subject? I am concerned because we later sampled surfaces on the DTI images, so I guess if the surf from the recon space is not correctly displayed on the DTI images, then my sampling is probably wrong too? The tracts are correctly displayed on the native DTI images, but if I want to display them on the anat space then it is not correct. Thanks for your help Celine
I concur. If this is the lowb.nii.gz from trac-all and brainmask.mgz from recon-all, they will be in their respective native spaces, and thus I wouldn't expect them to be registered to each other.
On the other hand, any brain masks that trac-all saves under dlabel/diff/ are in diffusion space, so those can be viewed with lowb.nii.gz without a registration file.
On Fri, 28 Feb 2014, Douglas N Greve wrote:
In general you should use a registration file when viewing your results. In many cases, it may look like it is in registration with out a registration file. This can happen if you acquired your anatomical and DTI data in the same session. For this subject, were they acquired in different sessions or was the subject removed and replaced back in the scanner? When you sample the data onto the surfaces, you should always use a registration file.
doug
On 02/27/2014 05:08 PM, Celine Louapre wrote:
Hi Anastasia and freesurfer experts I am having some troubles with the registration of DTI images processed with tracula for one subject. When I load the lowb.nii.gz on freeview together with brainmask, it is not registered, but when I am loading it with the registration matrix anatorig2diff.bbr.dat, it is correctly registered. I don't have to specify the registration file for the other subjects, is that an issue of this particular subject? I am concerned because we later sampled surfaces on the DTI images, so I guess if the surf from the recon space is not correctly displayed on the DTI images, then my sampling is probably wrong too? The tracts are correctly displayed on the native DTI images, but if I want to display them on the anat space then it is not correct. Thanks for your help Celine
Thnak you very much for clarifying this. So recon-all and trac-all outputs are all in their own native space.
Now if I need to sample surfaces on the diffusion images based on recons surface, I need to provide the /dmri/xfms/anatorig2diff registration matrix right? But it is not completely clear to me if anatorig2diff is the registration matrix from the anat to the diffusion space or the opposite? Because when I am loading brainmask from recon-all, then loading lowb.nii.gz using the anatorig2diff registration file, the registration is fine (and especially now that I have targeted a subject from whom the 2 spaces are really different, it is easier to figure out about registration). So anatorig2diff means diffusion space to anat space? Thanks a lot Celine
I concur. If this is the lowb.nii.gz from trac-all and brainmask.mgz from recon-all, they will be in their respective native spaces, and thus I wouldn't expect them to be registered to each other.
On the other hand, any brain masks that trac-all saves under dlabel/diff/ are in diffusion space, so those can be viewed with lowb.nii.gz without a registration file.
On Fri, 28 Feb 2014, Douglas N Greve wrote:
In general you should use a registration file when viewing your results. In many cases, it may look like it is in registration with out a registration file. This can happen if you acquired your anatomical and DTI data in the same session. For this subject, were they acquired in different sessions or was the subject removed and replaced back in the scanner? When you sample the data onto the surfaces, you should always use a registration file.
doug
On 02/27/2014 05:08 PM, Celine Louapre wrote:
Hi Anastasia and freesurfer experts I am having some troubles with the registration of DTI images processed with tracula for one subject. When I load the lowb.nii.gz on freeview together with brainmask, it is not registered, but when I am loading it with the registration matrix anatorig2diff.bbr.dat, it is correctly registered. I don't have to specify the registration file for the other subjects, is that an issue of this particular subject? I am concerned because we later sampled surfaces on the DTI images, so I guess if the surf from the recon space is not correctly displayed on the DTI images, then my sampling is probably wrong too? The tracts are correctly displayed on the native DTI images, but if I want to display them on the anat space then it is not correct. Thanks for your help Celine
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
It is a registration file that goes from the anat to the orig space, but freeview (and mri_vol2surf) knows this and knows which direction to apply it to doug
On 02/28/2014 04:12 PM, Celine Louapre wrote:
Thnak you very much for clarifying this. So recon-all and trac-all outputs are all in their own native space.
Now if I need to sample surfaces on the diffusion images based on recons surface, I need to provide the /dmri/xfms/anatorig2diff registration matrix right? But it is not completely clear to me if anatorig2diff is the registration matrix from the anat to the diffusion space or the opposite? Because when I am loading brainmask from recon-all, then loading lowb.nii.gz using the anatorig2diff registration file, the registration is fine (and especially now that I have targeted a subject from whom the 2 spaces are really different, it is easier to figure out about registration). So anatorig2diff means diffusion space to anat space? Thanks a lot Celine
I concur. If this is the lowb.nii.gz from trac-all and brainmask.mgz from recon-all, they will be in their respective native spaces, and thus I wouldn't expect them to be registered to each other.
On the other hand, any brain masks that trac-all saves under dlabel/diff/ are in diffusion space, so those can be viewed with lowb.nii.gz without a registration file.
On Fri, 28 Feb 2014, Douglas N Greve wrote:
In general you should use a registration file when viewing your results. In many cases, it may look like it is in registration with out a registration file. This can happen if you acquired your anatomical and DTI data in the same session. For this subject, were they acquired in different sessions or was the subject removed and replaced back in the scanner? When you sample the data onto the surfaces, you should always use a registration file.
doug
On 02/27/2014 05:08 PM, Celine Louapre wrote:
Hi Anastasia and freesurfer experts I am having some troubles with the registration of DTI images processed with tracula for one subject. When I load the lowb.nii.gz on freeview together with brainmask, it is not registered, but when I am loading it with the registration matrix anatorig2diff.bbr.dat, it is correctly registered. I don't have to specify the registration file for the other subjects, is that an issue of this particular subject? I am concerned because we later sampled surfaces on the DTI images, so I guess if the surf from the recon space is not correctly displayed on the DTI images, then my sampling is probably wrong too? The tracts are correctly displayed on the native DTI images, but if I want to display them on the anat space then it is not correct. Thanks for your help 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 -
Douglas N Greve