Dear Freesurfers,
I have a question regarding how Freesurfer's paired glmfit and monte-carlo analysis compares with SPM8 GLM design analysis on cortical thickness. If I were to export thickness maps as nifti files and do a paired comparison on SPM8, would that be a fair comparison with Freesurfer or is Freesurfer's analysis more appropriate for surface maps such as cortical thickness?
Thanks Koushik
The simple GLM should be the same. When you convert to nifti, you can either leave it as a surface overlay or you can run mri_surf2vol to create an actual volume of thicknesses. The latter may change the values and so change the results. Cluster-based correction for multiple comparisons will be different/wrong without taking into account the surface geometry.
doug
On 12/11/2013 10:58 AM, Govindarajan, Koushik Athreya wrote:
Dear Freesurfers,
I have a question regarding how Freesurfer’s paired glmfit and monte-carlo analysis compares with SPM8 GLM design analysis on cortical thickness. If I were to export thickness maps as nifti files and do a paired comparison on SPM8, would that be a fair comparison with Freesurfer or is Freesurfer’s analysis more appropriate for surface maps such as cortical thickness?
Thanks
Koushik
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for the response Doug.
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, December 11, 2013 10:44 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] paired analysis of cortical thickness - Freesurfer group analysis vs. SPM8 analysis
The simple GLM should be the same. When you convert to nifti, you can either leave it as a surface overlay or you can run mri_surf2vol to create an actual volume of thicknesses. The latter may change the values and so change the results. Cluster-based correction for multiple comparisons will be different/wrong without taking into account the surface geometry.
doug
On 12/11/2013 10:58 AM, Govindarajan, Koushik Athreya wrote:
Dear Freesurfers,
I have a question regarding how Freesurfer's paired glmfit and monte-carlo analysis compares with SPM8 GLM design analysis on cortical thickness. If I were to export thickness maps as nifti files and do a paired comparison on SPM8, would that be a fair comparison with Freesurfer or is Freesurfer's analysis more appropriate for surface maps such as cortical thickness?
Thanks
Koushik
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://urldefense.proofpoint.com/v1/url?u=https://mail.nmr.mgh.harvard.edu/...
freesurfer@nmr.mgh.harvard.edu
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Douglas N Greve -
Govindarajan, Koushik Athreya