Prelimiaries

The following files should be available before preprocessing can begin:

1. All functional V*.img (and corresponding V*.hdr) files (session1/V*, session2/V*, etc)

2. The subject’s inplane (2D) anatomical volume images and its header:
anatomy/inplane/V001.img
anatomy/inplane/V001.hdr

3. Optionally, you may have an SPGR anatomical volume image and its header:
anatomy/SPGR/V001.img
anatomy/SPGR/V001.hdr

Verify that the files are OK before starting

a) Display the anatomical images and one of the functional images to verify they have the right orientation

in matlab:
>> spm fmri
click on “DISPLAY”

Select image : anatomy/inplane/V001.img, DONE

In the upper part of the screen, there should be 3 boxes showing the 3 orthogonal views of the image:
- the upper left box should look like a coronal view
- the lower left box should look like an axial (horizontal) view, with the front of the brain in the top of the box (or closest to the coronal box)
- the top right box should display a sagittal view of the brain, with the front of the brain on the left side of the box (or closest to the coronal box)

b) Compute the a minimum image of all functionals to verify that all of them have been reconstructed successfully

from the matlab prompt, type:
>> spm_imcalc_ui(”,’all_min.img’,'min(X)’,{1;0;4;0})

Select images to work on : session1/V*.img, session2/V*.img, etc…, DONE

This will produce an ‘all_min.img’ file in the current directory (the directory) from which you started matlab). Use the DISPLAY button to verify that this image looks like one of the functional images - this is one possibile way to check for recontruction obnormalities.

Instead of ‘min(X)’ in the above formula, your could specify ‘max(X)’ to produce a maximum image, or ’std(X)’ to produce a standard deviation image from those selected, in case you would like to compute something else other than the minimum:

>> spm_imcalc_ui(”,’all_max.img’,'max(X)’,{1;0;4;0})

>> spm_imcalc_ui(”,’all_std.img’,’std(X)’,{1;0;4;0})