The simplest way to visualize results is using MRIcroGL combined with SPM image calculations.
- Create an effect size map of areas of significant effects using SPM
- [[Optional]] Create a subfolder of the correction method ("V:\LinuxShare\FSL_FIRST\ID111N1045G2\L_Hipp\MNI\TIVagesex\vox\significant_cope")
- Determine the number of the variable you want to look at; variables are referred to in filenames as "stat1", "stat2",... etc.
- Copy the corrected p-value file (F statistic) and the glm parameter estimate ("cope" file) into the subfolder.
- Unzip the *.nii.gz files to create *.nii files (since SPM cannot read *.nii.gz)
- Open imcalc from the SPM menu (or use attached batch file - click Batch, load "job...*.mat" file)
- For imput files, select the glm cope tstat file first, then the corrp fstat file
- Set a filename ("cope_tstat1_p05" could mean parameter estimates of stat1 at p < 0.05)
- [[recommended]] Set the output directory to be the subfolder
- Set the equation to be "i1.*(i2>=0.95)"
- Set the type to be int32 or float32
- [[optional]] save the batch file
- Run; this will create a file with direction (t statistic) at areas found to be significant according to permutation F test.
Find the mask.nii.gz file in the vertex folder (like "V:\LinuxShare\FSL_FIRST\ID111N1045G2\L_Hipp\MNI\TIVagesex")
- Open in MRIcroGL
- Go to File Overlay
- Open the created file, and set the color
- If the file has both positive and negative effects, load twice and display separately