Hi Anastasia, This would be in diffusion space though. Since I converted all of my seeds to diffusion space.
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: Friday, September 05, 2014 11:32 AM To: Freesurfer support list Subject: Re: [Freesurfer] Tracula To view your label over the MNI average brain: fslview $FSLDIR/data/standard/MNI152_T1_1mm.nii.gz your_label_in_MNI_space.nii.gz -l Red There are no settings, other than choosing a different color for the label. On Fri, 5 Sep 2014, Emily Louise Belleau wrote: > 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 > > > _______________________________________________ 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
