You can't do it in tandem. The 2nd command should work, just don't include -surf or -label Also, when you do use -surf, you need a subject and a hemi, eg, -surf fsaverage lh
On 2/24/2021 12:03 PM, Erin Moe wrote: > 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 <erin....@colorado.edu> 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 > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
