Hi Anastasia,
Many thanks for your reply and help. I was wondering that instead to redo all the preprocessing and registration steps s mentioned on FSTutorial/Running Tracula: * Eddy-current correction * Intra-subject registration (diffusion data to T1) * Inter-subject registration (individual subject to a common space) * Creation of cortical and white-matter masks from FreeSurfer recons
I can use all this results from my DTI Data Analysis Preprocessing Stream as mentioned on the FSTutorial/Diffusion, by runningfirst the dt_recon (this is performing an Eddy-current correction) and then I resampled structural data in the Diffusion space (aparc+aseg2diff.mgz, wm2diff.mgz), then I applyed the mask to the diffusion data and removed the unwanted "noise", using the 'mri_mask' command to get the masked fractional anisotropy volume (fa-masked.mgz), adc-masked.mgz and then doing individual subject registration on the CVA space and get resampled int CVS space (fa-masked.ANAT+CVS-to-avg35.mgz) using the using mri_cvs_register.
I also have all the outputs mentioned under FSL's dtifit since I got them by running dt_recon.
So I wonder if is possible to perform a DTI probabilistic tractography using TRACULA by starting only from the last two steps mentioned in trac-all -prep: * Computing anatomical priors for WM pathways, Recontructing WM Pathways, then visualizing the WM pathways, and then doing only statistics. This is what I meant by my previous results.
Thank you for your time and help.
Antonella
________________________________ From: Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, March 28, 2012 2:07 PM Subject: Re: [Freesurfer] dt_recon and tractography
Trackvis does deterministic tractography, not probabilistic.
Which previous results do you want to use and why?
On Wed, 28 Mar 2012, Antonella Kis wrote:
Dear FS experts,
I would like to know if for a Diffusion tensor imaging (DTI) tractography study with TRACULA I can use my previous results from FSTutorial/Diffusion more exactly my results after running dt_recon and registrations on the CVS space. If not can you please advise me if for a DTI probabilistic tractography using my previous results as mentioned above I can use TracVis.
Thank you. Antonella
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi,
I would redo the processing for the Tracula processing as the FSL tools require your data to be in a certain orientation and ours don't so you might end up with some inconsistencies if you use the two packages together.
Lilla
On Wed, 28 Mar 2012, Antonella Kis wrote:
Hi Anastasia,
Many thanks for your reply and help. I was wondering that instead to redo all the preprocessing and registration steps s mentioned on FSTutorial/Running Tracula:
- Eddy-current correction
- Intra-subject registration (diffusion data to T1)
- Inter-subject registration (individual subject to a common space)
- Creation of cortical and white-matter masks from FreeSurfer recons
I can use all this results from my DTI Data Analysis Preprocessing Stream as mentioned on the FSTutorial/Diffusion, by running first the dt_recon (this is performing an Eddy-current correction) and then I resampled structural data in the Diffusion space (aparc+aseg2diff.mgz, wm2diff.mgz), then I applyed the mask to the diffusion data and removed the unwanted "noise", using the 'mri_mask' command to get the masked fractional anisotropy volume (fa-masked.mgz), adc-masked.mgz and then doing individual subject registration on the CVA space and get resampled int CVS space (fa-masked.ANAT+CVS-to-avg35.mgz) using the using mri_cvs_register.
I also have all the outputs mentioned under FSL's dtifit since I got them by running dt_recon.
So I wonder if is possible to perform a DTI probabilistic tractography using TRACULA by starting only from the last two steps mentioned in trac-all -prep:
- Computing anatomical priors for WM pathways, Recontructing WM Pathways, then visualizing the WM pathways, and then doing only statistics.
This is what I meant by my previous results.
Thank you for your time and help.
Antonella
From: Anastasia Yendiki ayendiki@nmr.mgh.harvard.edu To: Antonella Kis atorok9@yahoo.com Cc: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Sent: Wednesday, March 28, 2012 2:07 PM Subject: Re: [Freesurfer] dt_recon and tractography
Trackvis does deterministic tractography, not probabilistic.
Which previous results do you want to use and why?
On Wed, 28 Mar 2012, Antonella Kis wrote:
Dear FS experts,
I would like to know if for a Diffusion tensor imaging (DTI) tractography study with TRACULA I can use my previous results from FSTutorial/Diffusion more exactly my results after running dt_recon and registrations on the CVS space. If not can you please advise me if for a DTI probabilistic tractography using my previous results as mentioned above I can use TracVis.
Thank you. Antonella
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.
freesurfer@nmr.mgh.harvard.edu
-
Antonella Kis -
Lilla Zollei