Overlay fMRI activation map on DTI

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Overlay fMRI activation map on DTI

Luigi Pavone
Hi to all,
I want to overlay fMRI activation map(from SPM) on DTI and then try to calculate fiber on these regions in order to establish if there are fiber connections between these regions.
Is it possible? If so, where can I find tutorials to do this?
Thanks.

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Re: Overlay fMRI activation map on DTI

Sonia Pujol
Hi Luigi,

To visualize the fMRI activation map overlaid on DTI data, load the SPM volume in Background, and the Baseline or FA volume in Foreground, and fade between the two volumes.
To generate tracts, you can use the Editor module to threshold the SPM volume and create an fMRI label map, and the Labelmap Seeding module to generate tracts from the  fMRI labelmap.

The 3D Data Loading and Visualization tutorial shows how to visualize several volumes simultaneously, the Interactive Editing tutorial shows how to threshold a volume, and the labelmap seeding process is described in the 'Diffusion MRI' tutorial. You might be interested in the Neurosurgery Planning tutorial, which combines DTI and fMRI data.

I hope this helps,

Best,

Sonia

http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training


On 3/21/2011 12:11 PM, Luigi Pavone wrote:
Hi to all,
I want to overlay fMRI activation map(from SPM) on DTI and then try to calculate fiber on these regions in order to establish if there are fiber connections between these regions.
Is it possible? If so, where can I find tutorials to do this?
Thanks.
_______________________________________________ slicer-users mailing list [hidden email] http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users To unsubscribe: send email to [hidden email] with unsubscribe as the subject



  


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Re: Overlay fMRI activation map on DTI

inorton
Hi Luigi,

In case you are using SPM2 or earlier: Slicer doesn't know anything about the SPM flip convention and doesn't support SPM Analyze in a very straightforward way. It is possible to use it, but you have to at least reslice the fMRI into structural space (in SPM) and then center both images (in Slicer - because the origin information is not preserved). It may also be necessary to manually flip in Slicer depending on the spm.analyze.flip setting in spm_defaults. Needless to say, use with care.

>SPM5 nifti files should work fine. To use LabelMapSeeding as Sonia indicated you will need to resample the activation to match the resolution of the DTI.

-Isaiah

On Mon, Mar 21, 2011 at 1:26 PM, Sonia Pujol <[hidden email]> wrote:
Hi Luigi,

To visualize the fMRI activation map overlaid on DTI data, load the SPM volume in Background, and the Baseline or FA volume in Foreground, and fade between the two volumes.
To generate tracts, you can use the Editor module to threshold the SPM volume and create an fMRI label map, and the Labelmap Seeding module to generate tracts from theĀ  fMRI labelmap.

The 3D Data Loading and Visualization tutorial shows how to visualize several volumes simultaneously, the Interactive Editing tutorial shows how to threshold a volume, and the labelmap seeding process is described in the 'Diffusion MRI' tutorial. You might be interested in the Neurosurgery Planning tutorial, which combines DTI and fMRI data.

I hope this helps,

Best,

Sonia

http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training



On 3/21/2011 12:11 PM, Luigi Pavone wrote:
Hi to all,
I want to overlay fMRI activation map(from SPM) on DTI and then try to calculate fiber on these regions in order to establish if there are fiber connections between these regions.
Is it possible? If so, where can I find tutorials to do this?
Thanks.
_______________________________________________ slicer-users mailing list [hidden email] http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users To unsubscribe: send email to [hidden email] with unsubscribe as the subject



  

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Re: Overlay fMRI activation map on DTI

Luigi Pavone
Hi Isaiah,Sonia
Is there a way to resample SPM activation maps to match the resolution of DTI?
Thanks.
Best,
Luigi.
 

 

Date: Mon, 21 Mar 2011 14:15:38 -0400
From: [hidden email]
To: [hidden email]
CC: [hidden email]
Subject: Re: [slicer-users] Overlay fMRI activation map on DTI

Hi Luigi,

In case you are using SPM2 or earlier: Slicer doesn't know anything about the SPM flip convention and doesn't support SPM Analyze in a very straightforward way. It is possible to use it, but you have to at least reslice the fMRI into structural space (in SPM) and then center both images (in Slicer - because the origin information is not preserved). It may also be necessary to manually flip in Slicer depending on the spm.analyze.flip setting in spm_defaults. Needless to say, use with care.

>SPM5 nifti files should work fine. To use LabelMapSeeding as Sonia indicated you will need to resample the activation to match the resolution of the DTI.

-Isaiah

On Mon, Mar 21, 2011 at 1:26 PM, Sonia Pujol <[hidden email]> wrote:
Hi Luigi,

To visualize the fMRI activation map overlaid on DTI data, load the SPM volume in Background, and the Baseline or FA volume in Foreground, and fade between the two volumes.
To generate tracts, you can use the Editor module to threshold the SPM volume and create an fMRI label map, and the Labelmap Seeding module to generate tracts from the  fMRI labelmap.

The 3D Data Loading and Visualization tutorial shows how to visualize several volumes simultaneously, the Interactive Editing tutorial shows how to threshold a volume, and the labelmap seeding process is described in the 'Diffusion MRI' tutorial. You might be interested in the Neurosurgery Planning tutorial, which combines DTI and fMRI data.

I hope this helps,

Best,

Sonia

http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training



On 3/21/2011 12:11 PM, Luigi Pavone wrote:
Hi to all,
I want to overlay fMRI activation map(from SPM) on DTI and then try to calculate fiber on these regions in order to establish if there are fiber connections between these regions.
Is it possible? If so, where can I find tutorials to do this?
Thanks.
_______________________________________________ slicer-users mailing list [hidden email] http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users To unsubscribe: send email to [hidden email] with unsubscribe as the subject



_______________________________________________
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[hidden email]
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Re: Overlay fMRI activation map on DTI

Dominik Meier
Hi Luigi

yes, in principle the ResampleScalarVectorDWIVolume module should be able to tackle that. Depends on the way the extra (non-spatial) dimensions of the DTI and the fMRI volumes are encoded, however. 

 If using the DTI as resample reference is not successful, you may need to generate an intermediate volume. If you can send me two example images, I will try to figure it out for you (as part of our online registration support special ;-)


Best,
Dominik



On Mar 28, 2011, at 5:11 AM, Luigi Pavone wrote:

Hi Isaiah,Sonia
Is there a way to resample SPM activation maps to match the resolution of DTI?
Thanks.
Best,
Luigi.
 

 

Date: Mon, 21 Mar 2011 14:15:38 -0400
From: [hidden email]
To: [hidden email]
CC: [hidden email]
Subject: Re: [slicer-users] Overlay fMRI activation map on DTI

Hi Luigi,

In case you are using SPM2 or earlier: Slicer doesn't know anything about the SPM flip convention and doesn't support SPM Analyze in a very straightforward way. It is possible to use it, but you have to at least reslice the fMRI into structural space (in SPM) and then center both images (in Slicer - because the origin information is not preserved). It may also be necessary to manually flip in Slicer depending on the spm.analyze.flip setting in spm_defaults. Needless to say, use with care.

>SPM5 nifti files should work fine. To use LabelMapSeeding as Sonia indicated you will need to resample the activation to match the resolution of the DTI.

-Isaiah

On Mon, Mar 21, 2011 at 1:26 PM, Sonia Pujol <[hidden email]> wrote:
Hi Luigi,

To visualize the fMRI activation map overlaid on DTI data, load the SPM volume in Background, and the Baseline or FA volume in Foreground, and fade between the two volumes.
To generate tracts, you can use the Editor module to threshold the SPM volume and create an fMRI label map, and the Labelmap Seeding module to generate tracts from the  fMRI labelmap. 

The 3D Data Loading and Visualization tutorial shows how to visualize several volumes simultaneously, the Interactive Editing tutorial shows how to threshold a volume, and the labelmap seeding process is described in the 'Diffusion MRI' tutorial. You might be interested in the Neurosurgery Planning tutorial, which combines DTI and fMRI data.

I hope this helps,

Best,

Sonia

http://www.slicer.org/slicerWiki/index.php/Slicer_3.6:Training



On 3/21/2011 12:11 PM, Luigi Pavone wrote:
Hi to all,
I want to overlay fMRI activation map(from SPM) on DTI and then try to calculate fiber on these regions in order to establish if there are fiber connections between these regions.
Is it possible? If so, where can I find tutorials to do this?
Thanks.
_______________________________________________ slicer-users mailing list [hidden email] http://massmail.spl.harvard.edu/mailman/listinfo/slicer-users To unsubscribe: send email to [hidden email] with unsubscribe as the subject



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To unsubscribe: send email to [hidden email] with unsubscribe as the subject


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