Saturday, December 8, 2012

SPM Design Specification and Estimation

At long last, after several long minutes - perhaps hours - or grueling preprocessing, you are ready to specify your general linear model. The concept is straightforward enough: Specify when a certain condition happened, input how long that condition took to happen (zero duration in the case of an instantaneous event), and what kind of basis function you want to convolve with that condition. Basis functions is a topic all on its own (you'll find out more when you're older!), but for the time being, realize that the canonical hemodynamic response function will suffice for most of your cases; even though sometimes it is a laughably wrong assumption about the shape of your hemodynamic response. But hey, it's the best we've got.

More details on the ins and outs of model specification, along with an example of what might be going through your head as you do this, can be found in the following video.

1 comment:

  1. Dear Andrew
    First of all I want you to know that you are my role model on the fMRI field.For me your videos are milestones toward learning of this field.
    Secondly,while performing 1th level analysis on task fmri data on GLM I encountered an unknown error.I will be really grateful if you could help me on that.The error is as follows:
    Mapping files : Failed 'fMRI model specification'
    Error using read_hdr (line 62)
    Bad vox_offset (0) for "C:\Users\MAhsa\Documents\MATLAB\Q1_motor\201111\tfMRI_MOTOR_LRx001.img.
    In file "C:\Users\MAhsa\Documents\MATLAB\spm8 updated\@nifti\private\read_hdr.m"(v1143), function "read_hdr" at line 62.
    In file "C:\Users\MAhsa\Documents\MATLAB\spm8 updated\@nifti\nifti.m"(v4270), function "nifti" at line 27.
    In file "C:\Users\MAhsa\Documents\MATLAB\spm8 updated\spm_vol_nifti.m" (v1143), function "spm_vol_nifti" at line 16.
    In file "C:\Users\MAhsa\Documents\MATLAB\spm8 updated\spm_vol.m" (v4045), function "subfunc" at line 124.
    In file "C:\Users\MAhsa\Documents\MATLAB\spm8 updated\spm_vol.m" (v4045), function "subfunc1" at line 77.
    In file "C:\Users\MAhsa\Documents\MATLAB\spm8 updated\spm_vol.m" (v4045), function "subfunc2" at line 69.
    In file "C:\Users\MAhsa\Documents\MATLAB\spm8 updated\spm_vol.m" (v4045), function "spm_vol" at line 54.
    In file "C:\Users\MAhsa\Documents\MATLAB\spm8 updated\spm_fmri_spm_ui.m" (v4421), function "spm_fmri_spm_ui" at line 368.
    In file "C:\Users\MAhsa\Documents\MATLAB\spm8 updated\config\spm_run_fmri_spec.m" (v4185), function "spm_run_fmri_spec" at line 301.

    The following modules did not run:
    Failed: fMRI model specification

    Please note that I have successfully done this before without any errors!