extracting cluster into nii file (marsbar?)

[bio...@gmail.com]

Dear SnPM experts,
I ran SnPM analysis on both structural and functional data at cluster-level analysis.
How do I extract the significant clusters and save them as a nifti files so they can be used in an ROI analysis?
I had considered Marsbar which uses the design file as the input (SPM.mat) to get the cluster. However, if I use either the SnPM or SnPMcfg this won't work.

Any ideas?

(I have considered thresholding the t-map, but this would also include the non-significant clusters which is not what I want)

Your help would be much appreciated.
Thank you,
Francesca

[Thomas Nichols]

Oh dear!  I just realise this question never got answered. For the record...

On Mon, Apr 24, 2017 at 2:33 PM, <bio...@gmail.com> wrote:

Dear SnPM experts,
I ran SnPM analysis on both structural and functional data at cluster-level analysis.
How do I extract the significant clusters and save them as a nifti files so they can be used in an ROI analysis?

You can save the results under the "Inference" section, with : "Write thresholded/filtered statistic image". 

 

I had considered Marsbar which uses the design file as the input (SPM.mat) to get the cluster. However, if I use either the SnPM or SnPMcfg this won't work.

 

Indeed, there isn't a SPM compatible file to feed into Marsbar.  Hopefully the 'filtered' image is enough.  Also check out other SPM extensions http://www.fil.ion.ucl.ac.uk/spm/ext/  ... maybe bspmview?

-Tom

Any ideas?

(I have considered thresholding the t-map, but this would also include the non-significant clusters which is not what I want)

Your help would be much appreciated.
Thank you,
Francesca

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__________________________________________________________

Thomas Nichols, PhD

Professor of Neuroimaging Statistics

Nuffield Department of Population Health | University of Oxford

Big Data Institute | Li Ka Shing Centre for Health Information and Discovery

Old Road Campus | Headington | Oxford | OX3 7LF | United Kingdom

T: +44 1865 743590 | E: thomas....@bdi.ox.ac.uk

W: http://nisox.org | http://www.bdi.ox.ac.uk

[Brandon Ashinoff]

Hi,

I have a follow-up to this question.

I ran an SnPM 2nd level analysis and I have 3 significant clusters. The  "Write thresholded/filtered statistic image" extracts all three clusters into a single image.

Is there a way to extract the clusters into individual images?

Thanks!

Cheers,

Brandon

On Thursday, November 30, 2017 at 3:50:50 AM UTC-5 Thomas Nichols wrote:

Oh dear!  I just realise this question never got answered. For the record...

On Mon, Apr 24, 2017 at 2:33 PM, <bio...@gmail.com> wrote:

Dear SnPM experts,
I ran SnPM analysis on both structural and functional data at cluster-level analysis.
How do I extract the significant clusters and save them as a nifti files so they can be used in an ROI analysis?

You can save the results under the "Inference" section, with : "Write thresholded/filtered statistic image". 

 

I had considered Marsbar which uses the design file as the input (SPM.mat) to get the cluster. However, if I use either the SnPM or SnPMcfg this won't work.

 

Indeed, there isn't a SPM compatible file to feed into Marsbar.  Hopefully the 'filtered' image is enough.  Also check out other SPM extensions http://www.fil.ion.ucl.ac.uk/spm/ext/  ... maybe bspmview?

-Tom

Any ideas?

(I have considered thresholding the t-map, but this would also include the non-significant clusters which is not what I want)

Your help would be much appreciated.
Thank you,
Francesca

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Visit this group at https://groups.google.com/group/snpm-support.
To view this discussion on the web, visit https://groups.google.com/d/msgid/snpm-support/69b6172c-538b-4c38-88a5-efee62d1b78b%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Flora Bouchacourt]

Did you find a way to do that?

Thank you