SDM preparation
Preparing the folder
SDM software assumes that all files needed for a meta-analysis are in the same folder.
Image files
If group-level statistical parametric maps are available, it is highly recommended to use them instead of peak coordinates. These image files must be in NIfTI format, and can be easily adapted for us in SDM with the 'Convert images' utility. Note that conversion of NIfTI files from other software may sometimes fail, e.g. leading to blank or flipped images. We thus strongly recommend always checking with a brain viewer (e.g. MRICron, FSLView or SPM Display) that:
- The converted file is a correct brain image.
- The left and right sides are not flipped.
- The pre-processing peaks are similar to those reported in the manuscript.
In case of failure, you might try to firstly copy the original NIfTI file to the meta-analysis directory, secondly open and save the copy with MRICron, and finally convert it with SDM. This seems to fix small issues of the file which prevent a correct conversion by SDM.
In case that left and right sides are flipped, you can try to fix the issue with FSL ("fslswapdim [filename] -x y z [filename]"), MRICro ("Save as...": "Flip Left/Right") or SPM ("Display": "resize {x} = -1").
Text files
The peak coordinates of each study must be written in text files, whose name must be the name of the study plus one of the following extensions:
- .spm_mni.txt if SPM coordinates are in MNI space (e.g. Walker2004.spm_mni.txt).
- .spm_brett.txt if SPM coordinates were converted from MNI space to Talairach space using the Brett's conversion (e.g. Brown2009.spm_brett.txt).
- .spm_tal.txt if SPM coordinates are in correct Talairach space (e.g. Williams1999.tal.txt). This is uncommon or only used for special analyses, please double check whether you should use .spm_mni.txt or .spm_brett.txt.
- .fsl_mni.txt if FSL coordinates are in MNI space (e.g. Jones2006.spm_mni.txt).
- .fsl_brett.txt if FSL coordinates were converted from MNI space to Talairach space using the Brett's conversion (e.g. Taylor2002.spm_brett.txt).
- .fsl_tal.txt if FSL coordinates are in correct Talairach space (e.g. Davies2013.tal.txt). This is uncommonor only used for special analyses, please double check whether you should use .fsl_mni.txt or .fsl_brett.txt.
- .other_mni.txt if non-FSL non-SPM coordinates are in MNI space (e.g. Hall2004.spm_mni.txt).
- .other_brett.txt if non-SPM non-FSL coordinates were converted from MNI space to Talairach space using the Brett's conversion (e.g. Evans2005.other_brett.txt).
- .other_tal.txt if non-SPM non-FSL coordinates are in correct Talairach space (e.g. Wright2004.tal.txt).
Each coordinate must be written in a line using the following pattern: x,y,z,t where t is either a positive t-statitic or 'p' (positive difference, e.g. activation, patients > controls) or a negative t-statistic or 'n' (negative difference, e.g. deactivation, patients < controls), e.g.:
-8,46,3,3.42
12,2,2,-4.43
18,22,4,n
You can easily convert p-values and z-scores into t-statistics with the online Convert peaks utility.
To specify the folder
Press the button [Change meta-analysis]
or:
Select [Change meta-analysis] in the Meta-analyses menu, to open the following dialog:
