External Email - Use Caution Regarding alternatives: you could run something like mriqc (https://pypi.org/project/mriqc/) on the source nifti/dicom files. It includes SNR measures if I remember correctly.
Tim > On August 7, 2020 at 4:22 PM "Douglas N. Greve" <dgr...@mgh.harvard.edu> > wrote: > > > > It should be related to the SNR, but including it as a noise measure > regressor in a GLM sounds dicey to me. > > > On 8/6/2020 5:02 AM, Scheffler, F, Mev [fre...@sun.ac.za] wrote: > > > > External Email - Use Caution > > > > Dear FreeSurfer Devs > > > > I got a comment about including a SNR variable in my main stats > > analysis and so came across a Rosen et al 2018 paper which refers to > > the Euler number. I then checked the archives and came across a thread > > <https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg58748.html> > > where you say that in version 6.0 the numbers are included in the > > aseg.stats file, specifically as a global measure called SurfaceHoles. > > > > With regards to our QC procedures: We visually inspected all of our > > scans and then followed ENIGMA’s quality assessment protocols. We > > excluded scans with motion artefacts or poor-quality images and only > > included the data from the scans with acceptable or good quality > > segmentation. Outlier detection and the distribution of our data was > > also checked prior to analysis of the data. > > > > So, my question is, can I include the SurfaceHoles variable in my > > model as a proxy for SNR? Would that be sensible, or do you have an > > alternative suggestion? > > > > Thanks very much! > > > > Kind regards, > > > > Freda Scheffler > > > > PhD Candidate > > > > > > _______________________________________________ > > 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 -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
