External Email - Use Caution Thanks Martin,
I just want to clarify that this then is the correct workflow: 1). Import the table generated from *asegstats2table* (asegstats2table.long.table), and select the column pertaining to the ROIs and eTIV. 2). Add to this table any covariates, as well as the group and time columns. 3). Specify a group x time interaction contrast (e.g. CM.C = [0 0 0 0 0 0 0 0 0 0 0 0 1];). 4). Use the table (design matrix) to perform LME. Assuming the above is correct, Is there a FreeSurfer (or Matlab) function for point #4, or could this even be performed in a statistical package such as R? Dan On Mon, Jul 1, 2024 at 8:40 AM Reuter, Martin,Ph.D. <mreu...@mgh.harvard.edu> wrote: > Hi Dan, > > No, mris_preproc and also surf2surf are functions that work on surfaces. > You would just import the volume statistics into Matlab and fill the > corresponding columns in your matrix directly, similar to using co-variates > such as eTIV. > > Best, Martin > > > On 1. Jul 2024, at 14:03, Dan Levitas <djlevitas...@gmail.com> wrote: > > Hi Martin, > > I wanted to ping this thread again, to confirm that my proposed > mass-univariate workflow using the subcortical segmented ROIs is > appropriate for the LME longitudinal analysis. > > Thanks again. > > Dan > > On Thu, Jun 27, 2024 at 5:44 AM Dan Levitas <djlevitas...@gmail.com> > wrote: > >> Hi Martin, >> >> Thanks for your reply, it's good to know that the mass-univariate >> approach is still appropriate here. >> >> Since the aseg segmentations are volumetric, can I still use the >> *mris_preproc* and *mri_surf2surf* functions? If so, would the >> mri_preproc function look something like *mri_preproc --qdec-long >> /path/to/asegstats2table.long.table --target fsaverage --hemi rh --meas >> volume --out output_dir/rh.volume.mgh* >> >> If not, and I need separate functions, would *mri_surf2surf* be replaced >> by *mri_vol2surf*? >> >> >> >> >> On Thu, Jun 27, 2024 at 4:51 AM Reuter, Martin,Ph.D. < >> mreu...@mgh.harvard.edu> wrote: >> >>> Hi Dan, >>> >>> You could do either one. I would recommend the mass univariate for >>> multiple independent test with the same design. >>> >>> Best, Martin >>> >>> On 26. Jun 2024, at 17:20, Dan Levitas <djlevitas...@gmail.com> wrote: >>> >>> >>> I recently performed an LME longitudinal mass-univariate (surface) >>> analysis and am now trying to do something similar, but with subcortical >>> (aseg) ROIs instead. >>> >>> I first created an aseg table with the following command: >>> >>> >>> >>> >>> >>> * asegstats2table \ --sd $subjects_dir \ --qdec-long >>> /path/to/long.qdec.table.dat \ --segno 4 10 11 12 17 18 26 43 49 50 51 53 >>> 54 58 251 253 255 \ --stats aseg.stats \ --tablefile $output_file* >>> >>> >>> The LME tutorial ( >>> https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels) >>> provides information and examples of both a univariate and mass-univariate >>> approach. While univariate seems most appropriate in this case, the example >>> details design matrix setup and testing of a single ROI (hippocampus), >>> whereas I would like to assess several subcortical ROIs. >>> >>> Would I simply create a loop structure to set up design matrices for >>> each ROI (both hemispheres) and test them individually, or can I perform a >>> mass-univariate approach to assess all ROIs at once? >>> >>> Thanks, >>> >>> Dan >>> >>> >>> _______________________________________________ >>> 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 >>> The information in this e-mail is intended only for the person to whom >>> it is addressed. If you believe this e-mail was sent to you in error and >>> the e-mail contains patient information, please contact the Mass General >>> Brigham Compliance HelpLine at >>> https://www.massgeneralbrigham.org/complianceline < >>> https://www.massgeneralbrigham.org/complianceline> . >>> >> > The information in this e-mail is intended only for the person to whom it > is addressed. If you believe this e-mail was sent to you in error and the > e-mail contains patient information, please contact the Mass General > Brigham Compliance HelpLine at > https://www.massgeneralbrigham.org/complianceline . >
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