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Spatial preprocessing

This page describes the transforms applied to the image data of a single participant prior to statistical analysis.

Display

Display one of the functional image volumes using the Display button on the “Menu” window. Note the orbitofrontal and inferior temporal drop-out and ghosting. This can be seen more clearly by selecting Brighten from the Effects menu in the Colours menu from the SPM Figure tab at the top of the “Graphics” window.

Realignment

Under the spatial pre-processing section of the SPM base window select Realign (Est & Res) from the Realign pull-down on the “Menu” window. This will call up a realignment job specification in the batch editor window. Then

  • Highlight data, select New Session, then highlight the newly created Session option. There are two fMRI runs, so you need to do this twice.

  • For the first session, select Specify Files and use the SPM file selector to choose all of the functional image volumes for the first run. To select all the volumes in a file, change the field that says 1 to NaN.

  • For the second session, select Specify Files and use the SPM file selector to choose all of the functional image volumes for the second run.

  • The other options in the user interface can be left as they are.

  • Save the job file as e.g. realign_job.m. When saved as a .m file, the jobs are human readable text that can serve as a starting point for creating scripts. If you read the contents of realign_job.m in a text editor, the structure of the contents should be comparable to the structure shown in the batch editor. 

    matlabbatch{1}.spm.spatial.realign.estwrite.data = {
                                                    {'func\sub-XX_ses-mri_task-facerecognition_run-01_bold.nii'}
                                                    {'func\sub-XX_ses-mri_task-facerecognition_run-02_bold.nii'}
                                                    }';
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.quality = 0.95;
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.sep = 1.5;
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.fwhm = 1;
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.rtm = 1;
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.interp = 2;
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.wrap = [0 0 0];
matlabbatch{1}.spm.spatial.realign.estwrite.eoptions.weight = '';
matlabbatch{1}.spm.spatial.realign.estwrite.roptions.which = [2 1];
matlabbatch{1}.spm.spatial.realign.estwrite.roptions.interp = 4;
matlabbatch{1}.spm.spatial.realign.estwrite.roptions.wrap = [0 0 0];
matlabbatch{1}.spm.spatial.realign.estwrite.roptions.mask = 1;
matlabbatch{1}.spm.spatial.realign.estwrite.roptions.prefix = 'r';

  • Press the Run button in the batch editor window (green triangle).

This will run the realign job which will write realigned images into the folder where the functional images are. These new images will be prefixed with the letter “r”. SPM will then plot the estimated time series of translations and rotations. These data, the realignment parameters for each run, are also saved to a file called func/rp_sub-XX_ses-mri_task-facerecognition_run-XX_bold.txt, so that these variables can be used as regressors when fitting GLMs. This allows movements effects to be discounted when looking for brain activations.

In addition to resliced versions of the original images (func/rsub-XX_ses-mri_task-facerecognition_run-01_bold.nii and func/rsub-XX_ses-mri_task-facerecognition_run-02_bold.nii), SPM will also create a mean image (func/meansub-XX_ses-mri_task-facerecognition_run-01_bold.nii) which will be used in the next step of spatial processing - coregistration.

Coregistration

Select Coregister (Estimate) from the Coregister pull-down on the “Menu” window. This will call up the specification of a coregistration job in the batch editor window.

  • Highlight Fixed Image and then select the mean functional image func/meansub-XX_ses-mri_task-facerecognition_run-01_bold.nii.

  • Highlight Moved Image and then select the anatomical image anat/sub-XX-T1w.nii.

  • Press the Save button and save the job as coreg_job.m

  • Then press the Run button.

SPM will then coregister the anatomical image so that it matches the functional data (as far as possible using a rigid-body transform). SPM will have changed the header of the moved (anatomical) image to reflect its new position and orientation.

Segmentation

Press the Segment button on the “Menu” window. This will call up the specification of a segmentation job in the batch editor window. Highlight the Volumes field in Data > Channels and then select the subject’s coregistered anatomical image anat/sub-XX-T1w.nii. Change Save INU corrected so that it contains Save INU corrected instead of Save nothing. At the bottom of the list, select Forward in Deformation Fields. Save the job file as segment_job.m and then press the Run button. SPM will segment the structural image using the default tissue probability maps as priors. SPM will create, by default, gray and white matter images and an intensity non-uniformity corrected version of the image. These can be viewed using the Check Reg facility.

SPM will also write a spatial normalisation deformation field file anat/y_sub-XX-T1w.nii in the original anat folder. This will be used in the next section to spatially normalise the functional data.

Normalise

Select Normalise (Write) from the Normalise pull-down on the “Menu” window. This will call up the specification of a normalise job in the batch editor window.

  • Highlight Data, select New Subject.

  • Open Subject, highlight Deformation field and select the anat/y_sub-XX-T1w.nii file that you created in the previous section.

  • Highlight Images to write and select all of the resliced functional images (func/rsub-XX_ses-mri_task-facerecognition_run-01_bold.nii and func/rsub-XX_ses-mri_task-facerecognition_run-02_bold.nii). To select all the volumes in a file, change the field that says 1 to NaN.

  • Press Save, save the job as norm_func_job.m and then press the Run button.

SPM will then write spatially normalised versions of the images to the func folder. These files have the prefix w (func/wrsub-XX_ses-mri_task-facerecognition_run-01_bold.niiandfunc/wrsub-XX_ses-mri_task-facerecognition_run-02_bold.nii`).

If you wish to superimpose a subject’s functional activations on their own anatomy you will also need to apply the spatial normalisation parameters to their (intensity non-uniformity corrected) anatomical image. To do this

  • Select Normalise (Write), highlight Data, select New Subject.

  • Highlight Deformation field, select the anat/y_sub-XX-T1w.nii file that you created previously and press Done.

  • Highlight Images to Write, select the intensity non-uniformity corrected anatomical MRI anat/msub-XX-T1w.nii and press Done.

  • Open Writing Options, select voxel sizes and change the default [2 2 2] to [1 1 1] which better matches the original resolution of the images.

  • Save the job as norm_struct_job.m and press the Run button.

The spatially normalised image will be saved as anat/wmsub-XX-T1w.nii.

Smoothing

Press the Smooth button on the “Menu” window. This will call up the specification of a smooth job in the batch editor window.

  • Select Images to Smooth and then select the spatially normalised volumes created in the last section (func/wrsub-XX_ses-mri_task-facerecognition_run-01_bold.nii and func/wrsub-XX_ses-mri_task-facerecognition_run-02_bold.nii). To select all the volumes in a file, change the field that says 1 to NaN.

  • Save the job as smooth_job.m and press the Run button.

This will smooth the data by (the default) 8 mm in each direction, which will be saved as image files prefixed by s (func/swrsub-XX_ses-mri_task-facerecognition_run-01_bold.nii and func/swrsub-XX_ses-mri_task-facerecognition_run-02_bold.nii).