If your label is in diffusion space, then replace the MNI brain with any volume that's in diffusion space.
On Fri, 5 Sep 2014, Emily Louise Belleau wrote: > 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
