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Hi!!, I have a two time point brain dataset of a single patient. The data consists of structural and DTI for both timesteps. I run FreeSurfer on each timestep separately for generating brain surfaces. When I display the brain surfaces(from both timesteps) together, they were appearing unregistered. Then I figured out that I need to use*FreeSurfer Longitudinal*to fix the registration problem. If I use FreeSurfer longitudinal, then it will most likely register both time point data to a common template, and my registration problem will be solved. I also want to display fiber tracts generated from MRtrix3 along with the brain surfaces generated by FreeSurfer. The problem is that the DTI data will not be touched by FreeSurfer. I am anticipating that this will become a problem to display fibertracts and brain surface properly. Please see below table that shows the data discrepancy I am expecting:
|+----------------------------------+-----------------------------------+ | time t0 | time t1 | +----------------------------------+-----------------------------------+ | T1.nii(registered by FreeSurfer) | T1.nii (registered by FreeSurfer) | | DTI.nii (unregistered DTI image) | DTI.nii (unregistered DTI image) | +----------------------------------+-----------------------------------+ |
FreeSurfer only takes in the structural data for brain surface generation and it leaves the DTI image untouched. Later, the fiber tracts generated using MRtrix3 won’t align with the FreeSurfer surfaces. How can fix this problem? Do you think it is possible to fetch some transformation and apply to DTI fiber tracts to fix the issue?
Thanks in advance Reshma
Hi Reshma,
Yes, you would use the FreeSurfer Longitudinal pipeline to process the two structural timepoints for your subject. Try running dt_recon on your DTI data. For more information on the dt_recon command and diffusion analysis in Freesurfer please refer to these sites: dt_reconhttps://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon dMRI_Processinghttps://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0
Best, Jocelyn ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sherin Sugathan sherin.sugathan@uib.no Sent: Thursday, October 28, 2021 8:11 AM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Registering DTI fiber tracts (from MRtrix3) to FreeSurfer registered surfaces.
External Email - Use Caution
Hi!!, I have a two time point brain dataset of a single patient. The data consists of structural and DTI for both timesteps. I run FreeSurfer on each timestep separately for generating brain surfaces. When I display the brain surfaces(from both timesteps) together, they were appearing unregistered. Then I figured out that I need to use FreeSurfer Longitudinal to fix the registration problem. If I use FreeSurfer longitudinal, then it will most likely register both time point data to a common template, and my registration problem will be solved. I also want to display fiber tracts generated from MRtrix3 along with the brain surfaces generated by FreeSurfer. The problem is that the DTI data will not be touched by FreeSurfer. I am anticipating that this will become a problem to display fibertracts and brain surface properly. Please see below table that shows the data discrepancy I am expecting:
+----------------------------------+-----------------------------------+ | time t0 | time t1 | +----------------------------------+-----------------------------------+ | T1.nii(registered by FreeSurfer) | T1.nii (registered by FreeSurfer) | | DTI.nii (unregistered DTI image) | DTI.nii (unregistered DTI image) | +----------------------------------+-----------------------------------+
FreeSurfer only takes in the structural data for brain surface generation and it leaves the DTI image untouched. Later, the fiber tracts generated using MRtrix3 won’t align with the FreeSurfer surfaces. How can fix this problem? Do you think it is possible to fetch some transformation and apply to DTI fiber tracts to fix the issue?
Thanks in advance Reshma
To add on to that, dt_recon will register you DTI to the FreeSurfer anatomical analysis. It will on generate FA, diffusivity, etc. I don't know how to get that interfaced with output from MRtrix3
On 10/29/2021 5:09 PM, Mora, Jocelyn S. wrote:
Hi Reshma,
Yes, you would use the FreeSurfer Longitudinal pipeline to process the two structural timepoints for your subject. Try running dt_recon on your DTI data. For more information on the dt_recon command and diffusion analysis in Freesurfer please refer to these sites: dt_recon https://surfer.nmr.mgh.harvard.edu/fswiki/dt_recon dMRI_Processing https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DiffusionV6.0
Best, Jocelyn
*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Sherin Sugathan sherin.sugathan@uib.no *Sent:* Thursday, October 28, 2021 8:11 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* [Freesurfer] Registering DTI fiber tracts (from MRtrix3) to FreeSurfer registered surfaces.
External Email - Use Caution
Hi!!, I have a two time point brain dataset of a single patient. The data consists of structural and DTI for both timesteps. I run FreeSurfer on each timestep separately for generating brain surfaces. When I display the brain surfaces(from both timesteps) together, they were appearing unregistered. Then I figured out that I need to use*FreeSurfer Longitudinal*to fix the registration problem. If I use FreeSurfer longitudinal, then it will most likely register both time point data to a common template, and my registration problem will be solved. I also want to display fiber tracts generated from MRtrix3 along with the brain surfaces generated by FreeSurfer. The problem is that the DTI data will not be touched by FreeSurfer. I am anticipating that this will become a problem to display fibertracts and brain surface properly. Please see below table that shows the data discrepancy I am expecting:
|+----------------------------------+-----------------------------------+ | time t0 | time t1 | +----------------------------------+-----------------------------------+ | T1.nii(registered by FreeSurfer) | T1.nii (registered by FreeSurfer) | | DTI.nii (unregistered DTI image) | DTI.nii (unregistered DTI image) | +----------------------------------+-----------------------------------+ |
FreeSurfer only takes in the structural data for brain surface generation and it leaves the DTI image untouched. Later, the fiber tracts generated using MRtrix3 won’t align with the FreeSurfer surfaces. How can fix this problem? Do you think it is possible to fetch some transformation and apply to DTI fiber tracts to fix the issue?
Thanks in advance Reshma
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Mora, Jocelyn S. -
Sherin Sugathan