[Freesurfer] mri_vol2surf projection of white matter results

2013-09-03 Thread Robert Schulz 
Dear Freesurfers, 

I transferred the white matter binary mask (derived from aseg, volume) to FSL 
and performed probabilistic tractography in it. 
Now I'd like to project the 'outer' white matter results (vol) onto the white 
surface. 

To test for the acuracy of this approach, I tried to project the white matter 
mask (binarized, volume) itself on the surface, proper projection should give 
only 1s (ones) on the surface, which holds true for the majority of vertices. 

I used the following command: mri_vol2surf --mov whitevolume.mgz --reg 
struct2freesurfer.dat --projdist-max 0 3 0.1 --interp nearest --hemi rh --out 
...

Is there a way to optimize this? The binarized white matter data (volume) is 
just below the white matter surface in most cases, sometimes, voxels are also 
above the surface.
If I try trilinear I get values far away from 1 (hence values which are not 
included in the primary data (=binarized mask). 

Looking forward to your suggestions. 

Thank you very much, 

Best 
Robert
--

Besuchen Sie uns auf: www.uke.de
_

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; 
Gerichtsstand: Hamburg
Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe 
Koch-Gromus, Joachim Prölß, Rainer Schoppik
_

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Re: [Freesurfer] mri_vol2surf projection of white matter results

2013-09-03 Thread Douglas N Greve 

you can sample under the wm surface by using negative proj fracts or 
proj dists
doug


On 09/03/2013 09:32 AM, Robert Schulz wrote:
> Dear Freesurfers,
> I transferred the white matter binary mask (derived from aseg, volume) 
> to FSL and performed probabilistic tractography in it.
> Now I'd like to project the 'outer' white matter results (vol) onto 
> the white surface.
> To test for the acuracy of this approach, I tried to project the white 
> matter mask (binarized, volume) itself on the surface, proper 
> projection should give only 1s (ones) on the surface, which holds true 
> for the majority of vertices.
> I used the following command: mri_vol2surf --mov whitevolume.mgz --reg 
> struct2freesurfer.dat --projdist-max 0 3 0.1 --interp nearest --hemi 
> rh --out ...
> Is there a way to optimize this? The binarized white matter data 
> (volume) is just below the white matter surface in most cases, 
> sometimes, voxels are also above the surface.
> If I try trilinear I get values far away from 1 (hence values which 
> are not included in the primary data (=binarized mask).
> Looking forward to your suggestions.
> Thank you very much,
> Best
> Robert
>
> Besuchen Sie uns auf: www.uke.de 
>
> 
>
> Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen 
> Rechts; Gerichtsstand: Hamburg
> Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. 
> Dr. Uwe Koch-Gromus, Joachim Prölß, Rainer Schoppik
>
> 
>
> SAVE PAPER - THINK BEFORE PRINTING
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] mri_vol2surf projection of white matter results

2013-09-03 Thread Robert Schulz 
Dear Freesurfers, 

I transferred the white matter binary mask (derived from aseg, volume) to FSL 
and performed probabilistic tractography in it. 
Now I'd like to project the 'outer' white matter results (vol) onto the white 
surface. 

To test for the acuracy of this approach, I tried to project the white matter 
mask (binarized, volume) itself on the surface, proper projection should give 
only 1s (ones) on the surface, which holds true for the majority of vertices. 

I used the following command: mri_vol2surf --mov whitevolume.mgz --reg 
struct2freesurfer.dat --projdist-max 0 3 0.1 --interp nearest --hemi rh --out 
...

Is there a way to optimize this? The binarized white matter data (volume) is 
just below the white matter surface in most cases, sometimes, voxels are also 
above the surface.
If I try trilinear I get values far away from 1 (hence values which are not 
included in the primary data (=binarized mask). 

Looking forward to your suggestions. 

Thank you very much, 

Best 
Robert
--

Besuchen Sie uns auf: www.uke.de
_

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; 
Gerichtsstand: Hamburg
Vorstandsmitglieder: Prof. Dr. Martin Zeitz (Vorsitzender), Prof. Dr. Dr. Uwe 
Koch-Gromus, Joachim Prölß, Rainer Schoppik
_

SAVE PAPER - THINK BEFORE PRINTING
___
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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.