Re: [Freesurfer] combine FEAT data with inflated ANATOMY to measure distances

2014-03-21 Thread Milde, Christopher 
Dear Doug,

I'm very thankful for your helpful comments! I will check the feat2surf script 
and apply it to map FSL-data in individual and common space (preconditions: 
existing FEATdir with non-smoothed EPI's and applied reg-feat2anat). I will 
make use of the -projfrac 0.5 to sample in the middle of the cortical ribbon 
(to account for drain vessel effects).

According to the intended distance measures, relative measures between peak 
voxels are also fine. So, maybe mris_pmake is still a good option...

Greets, Chris


Christopher Milde, M.Sc. Biol.
Institute for Cognitive and Clinical Neuroscience 
Central Institute of Mental Health Square J 5
68159 Mannheim, Germany 

Phone:  +49-621-1703-6313
E-mail:  christopher.mi...@zi-mannheim.de
Homepage:http://www.zi-mannheim.de/
Office:  Forschungs- und Verwaltungsgebäude, Room 230



-Ursprüngliche Nachricht-
Von: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve
Gesendet: Donnerstag, 20. März 2014 16:26
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] combine FEAT data with inflated ANATOMY to measure 
distances


1) Use the feat2surf script
2) I have not used mris_pmake myself. I'm guessing it will *work* on the sphere 
in that it will return a path, but the distances between vertices have no 
relationship to anatomy. It might fail on a flat map because it is a patch.

doug



On 03/20/2014 10:43 AM, Milde, Christopher wrote:
>
> Dear Surfers,
>
> At moment I'm dealing with a huge dataset, preprocessed (with and 
> without smoothing) and statistically analyzed in FSL FEAT.
>
> I used the reg-feat2anat to project functional EPI on inflated MPRAGE 
> (recon-all).
>
> Because *I'm interested in measuring Euclidian distances between peak 
> voxels*, I want to project *FEAT EPI-data on cortical flat maps
> (mris_flatten) or spherical surfaces*.
>
> èIs it possible to project FEAT-data on flat_maps?
>
> èDoes mris_pmake* works equally fine on different projections of the 
> EPI to ANATOMY (sphere, flat map) to measure peak/vertex distances?
>
> *https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017
> 866.html 
> <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2011-April/0178
> 66.html>
>
> I'm a quite Surfer-newby. So sorry for that maybe stupid question.
>
> Thank you in advance,
>
> Christopher
>
> *Christopher Milde, M.Sc. Biol.*
>
> Institute for Cognitive and Clinical Neuroscience
>
> Central Institute of Mental Health Square J 5
>
> 68159 Mannheim, Germany
>
> Phone: +49-621-1703-6313
>
> E-mail: christopher.mi...@zi-mannheim.de
>
> Homepage: http://www.zi-mannheim.de/ <http://www.zi-mannheim.de/>
>
> Office: Forschungs- und Verwaltungsgebäude, Room 230
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] combine FEAT data with inflated ANATOMY to measure distances

2014-03-20 Thread Milde, Christopher 
Dear Surfers,

At moment I'm dealing with a huge dataset, preprocessed (with and without 
smoothing) and statistically analyzed in FSL FEAT.

I used the reg-feat2anat to project functional EPI on inflated MPRAGE 
(recon-all).

Because I'm interested in measuring Euclidian distances between peak voxels, I 
want to project FEAT EPI-data on cortical flat maps (mris_flatten) or spherical 
surfaces.

è Is it possible to project FEAT-data on flat_maps?

è Does mris_pmake* works equally fine on different projections of the EPI to 
ANATOMY (sphere, flat map) to measure peak/vertex distances?



*https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017866.html


I'm a quite Surfer-newby. So sorry for that maybe stupid question...

Thank you in advance,

Christopher


Christopher Milde, M.Sc. Biol.
Institute for Cognitive and Clinical Neuroscience
Central Institute of Mental Health Square J 5
68159 Mannheim, Germany

Phone:  +49-621-1703-6313
E-mail:  christopher.mi...@zi-mannheim.de
Homepage:http://www.zi-mannheim.de/
Office:  Forschungs- und Verwaltungsgebäude, Room 230

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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] combine FEAT data with inflated ANATOMY to measure distances

2014-03-20 Thread Douglas N Greve 

1) Use the feat2surf script
2) I have not used mris_pmake myself. I'm guessing it will *work* on the 
sphere in that it will return a path, but the distances between vertices 
have no relationship to anatomy. It might fail on a flat map because it 
is a patch.

doug



On 03/20/2014 10:43 AM, Milde, Christopher wrote:
>
> Dear Surfers,
>
> At moment I’m dealing with a huge dataset, preprocessed (with and 
> without smoothing) and statistically analyzed in FSL FEAT.
>
> I used the reg-feat2anat to project functional EPI on inflated MPRAGE 
> (recon-all).
>
> Because *I’m interested in measuring Euclidian distances between peak 
> voxels*, I want to project *FEAT EPI-data on cortical flat maps 
> (mris_flatten) or spherical surfaces*.
>
> èIs it possible to project FEAT-data on flat_maps?
>
> èDoes mris_pmake* works equally fine on different projections of the 
> EPI to ANATOMY (sphere, flat map) to measure peak/vertex distances?
>
> *https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-April/017866.html
>  
> 
>
> I’m a quite Surfer-newby. So sorry for that maybe stupid question…
>
> Thank you in advance,
>
> Christopher
>
> *Christopher Milde, M.Sc. Biol.*
>
> Institute for Cognitive and Clinical Neuroscience
>
> Central Institute of Mental Health Square J 5
>
> 68159 Mannheim, Germany
>
> Phone: +49-621-1703-6313
>
> E-mail: christopher.mi...@zi-mannheim.de
>
> Homepage: http://www.zi-mannheim.de/ 
>
> Office: Forschungs- und Verwaltungsgebäude, Room 230
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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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.