Hi Anastasia, Yes my amygdala seed is in MNI space. When I used the MNI to diffusion.mat file in the dmri folder and placed it into FSL's probtractx, I developed a track that was in the wrong area of the brain, so I am thinking there is something wrong happening with the transformation to diffusion space.
Can I transform the amygdala mask into diffusion space prior to putting it into FSL's probtrackx viz bb register. If so, how might I go about doing that? Thanks so much for your help, Emily ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> Sent: Thursday, September 04, 2014 4:26 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Hi Emily - Is your amygdala seed ROI in MNI space? Only in that case the seed-to-diffusion transformation would be the MNI-to-diffusion transformation. a.y On Wed, 3 Sep 2014, Emily Louise Belleau wrote: > Hello, > > I did all of my DTI preprocessing through tracula. I now am using FSL > probtractx (which utilizes the bedpost stage output) to explore pathways from > the amygdala to the ventromedial prefontal cortex. > > When I used FSL's probtractx, when I viewed the tract. The tract was in the > wrong area of the brain. > > So, I think this may have something to do with the transfromation matrices I > gave it via tracula. > > *FSL asks for the seed to diffusion transformation matrix so that it can > convert your seed masks from MNI space to diffusion space. I gave the > transformation matrix in the dmri folder under xfms, titled > mni2diff.bbr.mat. I have a feeling this may be the issue. > > * I then tried to use the FLIRT registration tool through FSL to get the > appropriate transformation matrices. It asks for the bedpost directory. I > got an error saying it could not read my no_dif_brain_mask.nii. > > I am not sure what transformation matrix to give and was wondering if you > could give me some guidance. > > Thanks, > > Emily > > > _______________________________________________ > 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 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
