Rank: 1030 based on 63 downloads (last 30 days) and 7 files submitted
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Jeremy Manning

E-mail
Company/University
Princeton University

Personal Profile:

http://www.princeton.edu/~manning3

Professional Interests:
neuroscience, fmri, eeg, ecog, signal processing, graphics

 

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Files Posted by Jeremy View all
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(last 30 days)
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01 Jul 2013 Screenshot Generate synthetic fMRI data This program is useful for debugging fMRI analyses and models. Author: Jeremy Manning nifti, brain, data, synthetic, generate, simulation 27 11
  • 5.0
5.0 | 2 ratings
22 Feb 2013 Screenshot 2d and 3d brain plots Quickly and easily create 2d and 3d plots of fMRI data. Author: Jeremy Manning fmri, pcolor, 2d, 3d, brain, plot 12 2
  • 5.0
5.0 | 1 rating
04 Jan 2013 Screenshot "Chuck Close-ify" an image Create Chuck Close-style images from photographs and existing images. Author: Jeremy Manning chuck close, rectangle, circle, abstract, art, filter 1 0
21 Sep 2012 Screenshot sanePColor Wrapper for pcolor that behaves similarly to imagesc. Squash OS X Preview's "blurry image" bug! Author: Jeremy Manning pcolor, image, imagesc, semilogx, semilogy, loglog 14 4
  • 4.0
4.0 | 3 ratings
03 Mar 2012 slices Slice a tensor (n-d matrix) along the d^th dimension. Author: Jeremy Manning repmat, cellfun, arrayfun, join, fmri, tensor 3 0
Comments and Ratings by Jeremy View all
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29 Jul 2013 2d and 3d brain plots Quickly and easily create 2d and 3d plots of fMRI data. Author: Jeremy Manning

Hi David,

I would be happy to help. Can you please either describe your data in more detail or send me an example that triggers this error?

Note that if you set erode_layers too large, you will encounter an error, since only as many layers as exist may be stripped off of the brain image.

23 Dec 2012 Generate synthetic fMRI data This program is useful for debugging fMRI analyses and models. Author: Jeremy Manning

Hi Nes,

You're having trouble downloading the brain plots package? You should add a comment to that submission page, not this one. But if you just click the "Download Submission" link and unzip the file you download, all of the .m files should be in the resulting folder. I just re-downloaded that package to verify, and it looks OK to me...

21 Sep 2012 sanePColor Wrapper for pcolor that behaves similarly to imagesc. Squash OS X Preview's "blurry image" bug! Author: Jeremy Manning

Hi Jette, thanks for your feedback. I have corrected the issue you described (the new version should appear shortly).

11 May 2012 Generate synthetic fMRI data This program is useful for debugging fMRI analyses and models. Author: Jeremy Manning

The "data" variable contains the images for each trial specified by the design matrix (see above). That's what you pass to plot_brain2d or plot_brain3d. The 2d plots usually work better for viewing the synthetic data. This is because, whereas in real data "interesting stuff" often happens on the outer surface, in the synthetic data the sources are equally likely to be anywhere within the brain volume.

Let's say you want to generat a simple dataset with two trials, one unique source active per trial, and infinite signal-to-noise:

[data,cov_images] = generate_data(meta,eye(2),inf);

To generate 2d plot of first trial using default settings (requires installing http://www.mathworks.com/matlabcentral/fileexchange/36139-2d-and-3d-brain-plots), use:

plot_brain2d(data{1},meta);

To generate a 3d plot of second trial using default settings, use:

plot_brain3d(data{2},meta);

In each of the above examples, "meta" is the matrix included with the download of this package. (See documentation for additional details on the meta matrix.)

10 May 2012 Generate synthetic fMRI data This program is useful for debugging fMRI analyses and models. Author: Jeremy Manning

Hi ladyme,

To plot the images, you can use http://www.mathworks.com/matlabcentral/fileexchange/36139-2d-and-3d-brain-plots

Comments and Ratings on Jeremy's Files View all
Updated File Comment by Comments Rating
30 Jul 2013 2d and 3d brain plots Quickly and easily create 2d and 3d plots of fMRI data. Author: Jeremy Manning Cahn, David

29 Jul 2013 2d and 3d brain plots Quickly and easily create 2d and 3d plots of fMRI data. Author: Jeremy Manning Manning, Jeremy

Hi David,

I would be happy to help. Can you please either describe your data in more detail or send me an example that triggers this error?

Note that if you set erode_layers too large, you will encounter an error, since only as many layers as exist may be stripped off of the brain image.

26 Jul 2013 2d and 3d brain plots Quickly and easily create 2d and 3d plots of fMRI data. Author: Jeremy Manning Cahn, David

Hi,

I downloaded your code, but when I run brain_plot3d_alt, it prints a 2D image instead of a 3D image. I'm using the standard MNI brain...

Also, every time I try to put in an input for erode_layers the code throws an error. What's going wrong?

Thanks.

10 Jun 2013 sanePColor Wrapper for pcolor that behaves similarly to imagesc. Squash OS X Preview's "blurry image" bug! Author: Jeremy Manning Wang, David

x and y have to be row vectors. To be more flexible, replace in the linexpand function

x = 1:length(y);
p = polyfit(1:length(y),y,1);

with

x = reshape(1:length(y),[size(y)]);
p = polyfit(x,y,1);

21 Jan 2013 Generate synthetic fMRI data This program is useful for debugging fMRI analyses and models. Author: Jeremy Manning King, Edward

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Top Tags Applied by Jeremy
fmri, brain, image, nifti, pcolor
Files Tagged by Jeremy View all
Updated   File Tags Downloads
(last 30 days)
Comments Rating
01 Jul 2013 Screenshot Generate synthetic fMRI data This program is useful for debugging fMRI analyses and models. Author: Jeremy Manning nifti, brain, data, synthetic, generate, simulation 27 11
  • 5.0
5.0 | 2 ratings
22 Feb 2013 Screenshot 2d and 3d brain plots Quickly and easily create 2d and 3d plots of fMRI data. Author: Jeremy Manning fmri, pcolor, 2d, 3d, brain, plot 12 2
  • 5.0
5.0 | 1 rating
04 Jan 2013 Screenshot "Chuck Close-ify" an image Create Chuck Close-style images from photographs and existing images. Author: Jeremy Manning chuck close, rectangle, circle, abstract, art, filter 1 0
21 Sep 2012 Screenshot sanePColor Wrapper for pcolor that behaves similarly to imagesc. Squash OS X Preview's "blurry image" bug! Author: Jeremy Manning pcolor, image, imagesc, semilogx, semilogy, loglog 14 4
  • 4.0
4.0 | 3 ratings
03 Mar 2012 slices Slice a tensor (n-d matrix) along the d^th dimension. Author: Jeremy Manning repmat, cellfun, arrayfun, join, fmri, tensor 3 0

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