Hi Anastasia,
This would be in diffusion space though. Since I converted all of my seeds to diffusion space.
Emily ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki ayendiki@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki ayendiki@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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Anastasia Yendiki ayendiki@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
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