Rank: 51 based on 715 downloads (last 30 days) and 5 files submitted
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Jimmy Shen

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Company/University
Rotman Research Institute

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http://research.baycrest.org/~jimmy

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Files Posted by Jimmy View all
Updated   File Tags Downloads
(last 30 days)
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07 Mar 2013 Screenshot Tools for NIfTI and ANALYZE image Load, save, make, reslice, view (and edit) both NIfTI and ANALYZE data on any platform Author: Jimmy Shen analyze, niftl, nifti, image, medical, isotropic 600 109
  • 4.61765
4.6 | 37 ratings
04 Dec 2012 geotiffwrite Write a 2D or 3D array to a single or multi-band GeoTIFF file Author: Jimmy Shen earth sciences, dem, earth science, gps, gis, image 46 20
  • 4.88889
4.9 | 9 ratings
22 Feb 2011 Load BIOPAC ACQ (AcqKnowledge for PC) data Load BIOPAC's *.acq file (AcqKnowledge for Windows data format). Author: Jimmy Shen medical, biopac acqknowledge, acq, eeg, file, data 33 15
  • 4.625
4.6 | 8 ratings
16 Apr 2009 Screenshot Resampling volume or image with affine matrix Use affine matrix to convert 3D vol or 2D img to orthogonal one with corresponding affine matrix. Author: Jimmy Shen affine, 2d, 3d, image, volume, mapping 22 7
  • 4.5
4.5 | 4 ratings
22 Aug 2008 Screenshot 3D Bresenham's line generation Generate X Y Z coordinates of a 3D Bresenham's line between two given points Author: Jimmy Shen specialized, plotting, 3d, bresenham algorithm, raster, line 14 1
  • 4.0
4.0 | 1 rating
Comments and Ratings by Jimmy View all
Updated File Comments Rating
14 Sep 2012 Tools for NIfTI and ANALYZE image Load, save, make, reslice, view (and edit) both NIfTI and ANALYZE data on any platform Author: Jimmy Shen

Hi Zhi:

"collapse_nii_scan.m" will do the job.

Hi Samiy:

This tool can not be used to extract spinal cord. However, once you extracted it and saved into another Analyze/NIfTI file, this tool can load the data into MATLAB for further processing.

11 Jul 2012 Tools for NIfTI and ANALYZE image Load, save, make, reslice, view (and edit) both NIfTI and ANALYZE data on any platform Author: Jimmy Shen

Received the image, and it is a special RGB data type one. The nii.img ranges from 0 to 1 as usual, but the output value needs to be scaled by (glmax-glmin)+glmin.

10 Jul 2012 Tools for NIfTI and ANALYZE image Load, save, make, reslice, view (and edit) both NIfTI and ANALYZE data on any platform Author: Jimmy Shen

Would you please send me this image, so I can take a look into it for you tomorrow afternoon.

30 Apr 2012 Tools for NIfTI and ANALYZE image Load, save, make, reslice, view (and edit) both NIfTI and ANALYZE data on any platform Author: Jimmy Shen

Sure Mark. You need a reference image by the way, so you can see what will happen before and after you apply the transformation matrix. Here's the example:

1. Download "avg152T1_RL_nifti.nii" from NIfTI site. I use it as reference image.

2. View how the reference image looks like: nii=load_nii('avg152T1_RL_nifti.nii');
view_nii(nii);

3. Assume that I have a Transformation Matrix, which will let the reference image turn 30 degree counter-clockwise on XY plane, here will be the matrix: T=[cos(pi/6) -sin(pi/6) 0; sin(pi/6) cos(pi/6) 0; 0 0 1];

4. Get old_xyz from reference image: rl=load_untouch_nii('avg152T1_RL_nifti.nii');
old_xyz=[rl.hdr.hist.srow_x(1:3);rl.hdr.hist.srow_y(1:3);rl.hdr.hist.srow_z(1:3)];

5. Apply your transformation matrix, and save new_xyz into a new image: new_xyz=T*old_xyz; rl.hdr.hist.srow_x(1:3)=new_xyz(1,:); rl.hdr.hist.srow_y(1:3)=new_xyz(2,:); rl.hdr.hist.srow_z(1:3)=new_xyz(3,:); save_untouch_nii(rl, 'rl30.nii'); Now you already have the "rl30.nii", which is a transformed NIfTI image can be used anywhere.

6. In order to view this image using my toolbox, you need to reslice it: reslice_nii('rl30.nii', 'rl30b.nii'); Now, you can load and view the rotated image: rl30b=load_nii('rl30b.nii'); view_nii(rl30b);

Hopefully this answers your questions.

26 Apr 2012 geotiffwrite Write a 2D or 3D array to a single or multi-band GeoTIFF file Author: Jimmy Shen

You need to use MATLAB's geotiffread to read L7 file into matrix, with all attributes. Then find out the index of your sub-region, and assign the sub-region to a new matrix. You can now use the make_option option in my package to select optional fields. However, you need to match the attributes that you read, and select the correct fields by yourself in order to create the optional fields to be used in my geotiffwrite. Since I don't have Mapping toolbox, I am afraid that I cannot provide you with more details.

Comments and Ratings on Jimmy's Files View all
Updated File Comment by Comments Rating
02 May 2013 Tools for NIfTI and ANALYZE image Load, save, make, reslice, view (and edit) both NIfTI and ANALYZE data on any platform Author: Jimmy Shen Guevara Codina, Edgar

12 Dec 2012 geotiffwrite Write a 2D or 3D array to a single or multi-band GeoTIFF file Author: Jimmy Shen Sunke

thanks for this export option! It helps sharing my MatLab data with colleagues that do not use MatLab, but ArcGIS, a lot !

18 Oct 2012 Tools for NIfTI and ANALYZE image Load, save, make, reslice, view (and edit) both NIfTI and ANALYZE data on any platform Author: Jimmy Shen Bilgic, Berkin

14 Sep 2012 Tools for NIfTI and ANALYZE image Load, save, make, reslice, view (and edit) both NIfTI and ANALYZE data on any platform Author: Jimmy Shen Shen, Jimmy

Hi Zhi:

"collapse_nii_scan.m" will do the job.

Hi Samiy:

This tool can not be used to extract spinal cord. However, once you extracted it and saved into another Analyze/NIfTI file, this tool can load the data into MATLAB for further processing.

11 Sep 2012 Tools for NIfTI and ANALYZE image Load, save, make, reslice, view (and edit) both NIfTI and ANALYZE data on any platform Author: Jimmy Shen Zhi

In FSL, there is a tool called avwmerge, which binds several hdr or nii files into a single hdr or nii file. Some existing applications only use the single hdr/nii file as input. Could I find similar function in your tool box? Many thanks.

Top Tags Applied by Jimmy
image, 3d, format, medical, save
Files Tagged by Jimmy View all
Updated   File Tags Downloads
(last 30 days)
Comments Rating
07 Mar 2013 Screenshot Tools for NIfTI and ANALYZE image Load, save, make, reslice, view (and edit) both NIfTI and ANALYZE data on any platform Author: Jimmy Shen analyze, niftl, nifti, image, medical, isotropic 600 109
  • 4.61765
4.6 | 37 ratings
04 Dec 2012 geotiffwrite Write a 2D or 3D array to a single or multi-band GeoTIFF file Author: Jimmy Shen earth sciences, dem, earth science, gps, gis, image 46 20
  • 4.88889
4.9 | 9 ratings
22 Feb 2011 Load BIOPAC ACQ (AcqKnowledge for PC) data Load BIOPAC's *.acq file (AcqKnowledge for Windows data format). Author: Jimmy Shen medical, biopac acqknowledge, acq, eeg, file, data 33 15
  • 4.625
4.6 | 8 ratings
16 Apr 2009 Screenshot Resampling volume or image with affine matrix Use affine matrix to convert 3D vol or 2D img to orthogonal one with corresponding affine matrix. Author: Jimmy Shen affine, 2d, 3d, image, volume, mapping 22 7
  • 4.5
4.5 | 4 ratings
22 Aug 2008 Screenshot 3D Bresenham's line generation Generate X Y Z coordinates of a 3D Bresenham's line between two given points Author: Jimmy Shen specialized, plotting, 3d, bresenham algorithm, raster, line 14 1
  • 4.0
4.0 | 1 rating

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