Check your data
Although the processing is automated, this doesn’t mean that things will never go wrong. Your data may have a problem – scanning glitches or excessive subject movement, for example – or there maybe something wrong with the analysis. Just as you would when doing it by hand, you should check your data at various stages.
Diagnostic JPEGs
One way of checking your data is to check through the images dumped in the analysed study, subject and block directories. These files begin with “diagnostic_aamod” end have a “.jpg” suffix. These are described in the table below.
Current output is all graphical, in the form of JPEG files. These may be viewed using a Windows graphics viewer, or with xv on unix. Examples are below
Name |
File directory |
Description |
diagnostic_aamod_anato3d_rawmean |
Session |
raw mean as generated by anato3d |
diagnostic_aamod_anato3d_rawvar |
Session |
raw variance as generated by anato3d |
diagnostic_aamod_tsdiffana |
Session |
output from tsdiffana |
diagnostic_aamod_realign |
Subject |
realignment display from SPM |
diagnostic_aamod_undist |
Subject |
evaluation of undistortion. Top pair of images are in distorted space and should be similar in shape and coregistered with each other. Left is distorted fieldmap magnitude, right is raw EPI. Bottom two images are in undistorted space and should be similar in shape and coregistered with each other, although not necessarily with the top two images. |
diagnostic_aamod_coreg |
Subject |
SPM output from coregistration of structural and undistorted EPI |
diagnostic_aamod_norm |
Subject |
SPM output from normalisation |
Rhodri Cusack, MRC CBU, Cambridge<rhodri DOT cusack AT mrc-cbu DOT cam DOT ac DOT uk>. Thank you to Matthew Brett, Jessica Grahn, Daniel Mitchell, Rik Henson & Matt Davis, who contributed to the code and this manual.