External Email - Use Caution Hi Doug, Thank you for the advice! I tried plugging the output of aparc2stats into mri_glmfit both in tandem with —y (mri_preproc_output).mgh as well as on its own and got an error message from mri_reshape saying the elements cannot be changed nv1=163842, nv1=2. This was an iteration of the table with one data column for the thickness of an ROI, however, I also got the same error with the full table. This is also the same table we used in SPSS for a linear regression there.
Terminal inputs: mri_glmfit —y lh.thickness.inflammatory.10.mgh —fsgd inflammatory_markers.fsgd —C Inflammatory_group.mtx —C group_inflammatory.mtx —surf fsaverage —table entorhinal_table.dat —label entorhinal.label —glmdir Inflammatory_entorhinal.lh.thickness.10.glmdir mri_glmfit —fsgd inflammatory_markers.fsgd —C Inflammatory_group.mtx —C group_inflammatory.mtx —surf fsaverage —table aparc_table.dat —label entorhinal.label —glmdir Inflammatory_entorhinal.lh.thickness.10.glmdir Thanks! Erin > On Feb 18, 2021, at 11:15 AM, Erin Moe <[email protected]> wrote: > > Hi Freesurfer experts, > I’ve been running mri_glmfit and QDEC to investigate the effect of > inflammatory markers on cortical thickness and don’t really get much. > However, when I extract the cortical thickness values (with > aparc/asegstats2table) and run a linear regression with those same > inflammatory markers in SPSS, I get several significant results. I’m assuming > it might be due to me setting up the QDEC/mri_glmfit analysis wrong. > > For QDEC I have a two column .dat file with the subject IDs in the FSID > column and the inflammatory markers for each participant in the other column > and running the QDEC thickness analysis on that and I don’t get much in terms > of results. > > For mri_glmfit I used an FSGD file set up just like the .dat file for QDEC > with the exception of formatting. However, we wanted to constrain the > analysis to an ROI (entorhinal in this case), I ran mris_preproc with the > following command: > mris_preproc —fsgd inflammatory_markers.fsgd —cache-in > thickness.fwhm10.fsaverage —target fsaverage —hemi lh —out > lh.thickness.inflammatory.10.mgh > > Then fed that output into mri_glmfit as: > mri_glmfit —y lh.thickness.inflammatory.10.mgh —fsgd > inflammatory_markers.fsgd —C Inflammatory_group.mtx —C group_inflammatory.mtx > —surf fsaverage —label entorhinal.label —glmdir > Inflammatory_entorhinal.lh.thickness.10.glmdir > The results from this look the same as the QDEC analysis but just masked out > for the entorhinal ROI. So, to constrain the analysis to the ROI, I ran a > Monte Carlo correction with mri_surfcluster. > > So a few questions: > Would running mri_surfcluster on the sig.mgh output from the mri_glmfit > analysis actually constrain the analysis to the ROI specified? > > How can I get my results to match that of what I’m seeing in SPSS? > > Is my analysis set up correctly for what I’m trying to do? > > > > Thank you in advance for your patience with this lengthy inquiry. > > Best, > Erin > > > > _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
