Hi Freesurfers,
Does anyone know how to make an average activation map of two subjects without running a group analysis? I have 15 subjects that each have a pre and a post scan (30 scans total) and we would like to combine the pre and post bold runs for each subject to generate an averaged AllvFix activation map for each pair (so I would end up with 1 activation map per subject pair of the pre and post bold runs averaged together -- 15 maps total). Originally I tried treating each of my subject pairs as a group and ran isxconcat-sess and mri_glmfit on each pair (N=2), but because my N was so small the osgm map looked very strange and wispy.
Because I'm trying to combine a pre and post scan for the same subject, is it possible to register the post subject's bold scans to the pre subject (or vice versa) so that we can treat all the bold runs as one subject and run selxavg3-sess referencing the pre and post bold runs in the runlist file? Any clarification or suggestions would be greatly appreciated!
Thanks, Alex
Hi Alex, you're almost there. When you run your "group" analysis with mri_glmfit, perform a fixed effects analysis, something like
mri_glmfit --y ces.nii.gz --yffxvar ces.var.nii.gz --ffxdofdat ../ffxdof.dat ...
doug
On 08/23/2013 02:56 PM, Alexandra Tanner wrote:
Hi Freesurfers,
Does anyone know how to make an average activation map of two subjects without running a group analysis? I have 15 subjects that each have a pre and a post scan (30 scans total) and we would like to combine the pre and post bold runs for each subject to generate an averaged AllvFix activation map for each pair (so I would end up with 1 activation map per subject pair of the pre and post bold runs averaged together -- 15 maps total). Originally I tried treating each of my subject pairs as a group and ran isxconcat-sess and mri_glmfit on each pair (N=2), but because my N was so small the osgm map looked very strange and wispy.
Because I'm trying to combine a pre and post scan for the same subject, is it possible to register the post subject's bold scans to the pre subject (or vice versa) so that we can treat all the bold runs as one subject and run selxavg3-sess referencing the pre and post bold runs in the runlist file? Any clarification or suggestions would be greatly appreciated!
Thanks, Alex
Hi Alex, You may use mri_concat with --mean flag, or alternatively use fslmaths to compute the average. Maybe Doug or Bruce or others have better ideas. Hth, Shantanu
On Fri, August 23, 2013 2:56 pm, Alexandra Tanner wrote:
Hi Freesurfers,
Does anyone know how to make an average activation map of two subjects without running a group analysis? I have 15 subjects that each have a pre and a post scan (30 scans total) and we would like to combine the pre and post bold runs for each subject to generate an averaged AllvFix activation map for each pair (so I would end up with 1 activation map per subject pair of the pre and post bold runs averaged together -- 15 maps total). Originally I tried treating each of my subject pairs as a group and ran isxconcat-sess and mri_glmfit on each pair (N=2), but because my N was so small the osgm map looked very strange and wispy.
Because I'm trying to combine a pre and post scan for the same subject, is it possible to register the post subject's bold scans to the pre subject (or vice versa) so that we can treat all the bold runs as one subject and run selxavg3-sess referencing the pre and post bold runs in the runlist file? Any clarification or suggestions would be greatly appreciated!
Thanks, Alex
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Alexandra Tanner -
Douglas N Greve -
Shantanu Ghosh