Hi Anastasia, I am still having a bit of trouble understanding how to properly view my tract through fsl view.
What is the appropriate underlay to use/settings? Thanks again for your continued 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 4:54 PM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula Certainly you can, and it's a good idea for troubleshooting this. In FSL you can do it with: flirt -in your_label_in_MNI_space.nii.gz -out your_label_in_diff_space.nii.gz -ref dmri/lowb.nii.gz -applyxfm -init dmri/xfms/mni2diff.bbr.mat -interp nearestneighbour Then you can overlay the transformed label on some of the other inputs that you're giving probtrackx (e.g. a volume from the bedpostx directory) to make sure they look right in fslview. On Thu, 4 Sep 2014, Emily Louise Belleau wrote: > 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 > > > _______________________________________________ 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
