Re: [Freesurfer] FreeSurfer Labels To Diffusion Toolkit/TrackVis

[Yendiki, Anastasia]

Hi Katherine - If you mean the .trk format, that's not for storing labels, it's 
for storing tractography streamlines (i.e., a bunch of curves that are stored 
as sequences of x,y,z point coordinates). You can convert the FreeSurfer labels 
to nifti volumes, and see if the software that you're trying to use for graph 
analysis can read in the labels in that format.


TRACULA does not do whole brain tractography, it's for reconstructing specific 
pathways. If you want to do whole brain tensor tractography and save the 
results in .trk format, you can use the dtk/trackvis.


There are two different inputs that you need for your graph analysis, the 
tracts in .trk format and the labels that will be the end points of the tracts 
- you have to find out what the format of the latter needs to be.


a.y


From: Katherine Damme <katherine.da...@gmail.com>
Sent: Thursday, February 22, 2018 8:45:20 PM
To: Anastasia Yendiki; Freesurfer support list
Subject: FreeSurfer Labels To Diffusion Toolkit/TrackVis

Hello Everyone,

I would like to use the FreeSurfer labels for fMRI and DTI in graph theory 
analyses. I am attempting to use UMPC<https://github.com/jbrown81/umcp> to 
generate the graphs, which requires that the diffusion tensor imaging be in 
.dtk form. However, I have been struggling to get the FreeSurfer labels into 
the .dtk space.

While I have found this 
<https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransforms> 
website suggesting a method for moving from the dtk space to FreeSurfer, it 
doesn't appear to be a reversible process.

Leading me to ask:

1. Is there a way to generate graphs from TRACULA?

or

2. How can I transform the labels or dlabels into dtk space?

Thank you for any help on this topic!

Kate Damme
___
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] FreeSurfer Labels To Diffusion Toolkit/TrackVis

[Katherine Damme]

Hello Everyone,

I would like to use the FreeSurfer labels for fMRI and DTI in graph theory
analyses. I am attempting to use UMPC  to
generate the graphs, which requires that the diffusion tensor imaging be in
.dtk form. However, I have been struggling to get the FreeSurfer labels
into the .dtk space.

While I have found this
website
suggesting a method for moving from the dtk space to FreeSurfer, it doesn't
appear to be a reversible process.

Leading me to ask:

1. Is there a way to generate graphs from TRACULA?

or

2. How can I transform the labels or dlabels into dtk space?

Thank you for any help on this topic!

Kate Damme
___
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.