Contents

Dependencies:

% Matlab statistics toolbox
  % Matlab signal processing toolbox
  % Statistical Parametric Mapping (SPM) software https://www.fil.ion.ucl.ac.uk/spm/
  % For full functionality, the full suite of CANlab toolboxes is recommended. See here: Installing Tools

HOW TO WRITE FMRI_DATA TO IMAGE FILE ON DISK

% canlabcore fmri data objects can be easily written to standard image file
% formats.  The main function for this is write()

% this walkthrough shows how to do this for 1) a mask image, and 2) a
% statistic image

1) load sample mask

You will need the Neuroimaging_Pattern_Masks repository installed to find these images.

dat = load_image_set('bucknerlab'); % loads 7 masks from Yeo et al.

Loaded images:
/Users/torwager/Documents/GitHub/CanlabCore/CanlabCore/canlab_canonical_brains/Combined_multiatlas_ROI_masks/rBucknerlab_7clusters_SPMAnat_Other_combined.img

grab one image from those 7

oneimg = dat.get_wh_image(1);

write to file

see help for write() for more options

fname = 'dummy.nii';  % outname file name.  the extension (.nii, .img) determines the format.

write(oneimg, 'fname', fname);

Writing: 
dummy.nii

read back in and view to check its correct

orthviews(fmri_data(fname))

Using default mask: /Users/torwager/Documents/GitHub/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/brainmask.nii
loading mask. mapping volumes. 
checking that dimensions and voxel sizes of volumes are the same. 
Pre-allocating data array. Needed: 1409312 bytes
Loading image number:     1
Elapsed time is 0.020971 seconds.
Image names entered, but fullpath attribute is empty. Getting path info.

SPM12: spm_check_registration (v6245)              19:30:11 - 02/08/2018
========================================================================
Display <a href="matlab:spm_image('display','/Users/torwager/Documents/GitHub/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1');">/Users/torwager/Documents/GitHub/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1</a>
Grouping contiguous voxels:   3 regions

ans =

  1×1 cell array

    {1×3 region}

2) load sample statistical image

dat = load_image_set('kragelemotion'); % loads 7 masks from Kragel et al.

% grab one image from those 7
oneimg = dat.get_wh_image(1);

Loaded images:
/Users/torwager/Documents/GitHub/MasksPrivate/Masks_private/2015_Kragel_emotionClassificationBPLS/mean_3comp_amused_group_emotion_PLS_beta_BSz_10000it.img
/Users/torwager/Documents/GitHub/MasksPrivate/Masks_private/2015_Kragel_emotionClassificationBPLS/mean_3comp_angry_group_emotion_PLS_beta_BSz_10000it.img
/Users/torwager/Documents/GitHub/MasksPrivate/Masks_private/2015_Kragel_emotionClassificationBPLS/mean_3comp_content_group_emotion_PLS_beta_BSz_10000it.img
/Users/torwager/Documents/GitHub/MasksPrivate/Masks_private/2015_Kragel_emotionClassificationBPLS/mean_3comp_fearful_group_emotion_PLS_beta_BSz_10000it.img
/Users/torwager/Documents/GitHub/MasksPrivate/Masks_private/2015_Kragel_emotionClassificationBPLS/mean_3comp_neutral_group_emotion_PLS_beta_BSz_10000it.img
/Users/torwager/Documents/GitHub/MasksPrivate/Masks_private/2015_Kragel_emotionClassificationBPLS/mean_3comp_sad_group_emotion_PLS_beta_BSz_10000it.img
/Users/torwager/Documents/GitHub/MasksPrivate/Masks_private/2015_Kragel_emotionClassificationBPLS/mean_3comp_surprised_group_emotion_PLS_beta_BSz_10000it.img

threshold at an arbitrary threshold. This will create a statistic_image

% keep values less than -.0005 or greater than .0005
si = threshold(oneimg, [-.0005 .0005], 'raw-outside');

% check that it looks fine
orthviews(si);

Keeping vals outside of -0.001 to 0.001: 474 elements remain

SPM12: spm_check_registration (v6245)              19:30:14 - 02/08/2018
========================================================================
Display <a href="matlab:spm_image('display','/Users/torwager/Documents/GitHub/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1');">/Users/torwager/Documents/GitHub/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1</a>
Grouping contiguous voxels:  83 regions

write to file

fname = 'dummy.nii';  % outname file name.  the extension (.nii, .img) determines the format.

write(si, 'fname', fname, 'thresh') % will write the *thresholded* image

Warning: Thresholding only works with statistic_image objects.
Writing: 
dummy.nii

read back in and view to check its correct

orthviews(fmri_data(fname))

Using default mask: /Users/torwager/Documents/GitHub/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/brainmask.nii
loading mask. mapping volumes. 
checking that dimensions and voxel sizes of volumes are the same. 
Pre-allocating data array. Needed: 188152 bytes
Loading image number:     1
Elapsed time is 0.008781 seconds.
Image names entered, but fullpath attribute is empty. Getting path info.

SPM12: spm_check_registration (v6245)              19:30:17 - 02/08/2018
========================================================================
Display <a href="matlab:spm_image('display','/Users/torwager/Documents/GitHub/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1');">/Users/torwager/Documents/GitHub/CanlabCore/CanlabCore/canlab_canonical_brains/Canonical_brains_surfaces/keuken_2014_enhanced_for_underlay.img,1</a>
Grouping contiguous voxels:  83 regions

ans =

  1×1 cell array

    {1×83 region}

Published with MATLAB® R2018a