intensity.deep and superficial are estimates of the intensity of the bottom of the cortex (deep) and the top of the cortex (superficial). These aren't generated by default, although we do have some tools for doing so.
cheers Bruce On Tue, 22 May 2012, Douglas N Greve wrote: > > > On 05/22/2012 04:18 PM, Mahinda Yogarajah wrote: >> Hi, >> >> Sorry to re-post but I wanted to amend my questions on the basis of >> further reading I have done in the forum. Ignore questions 1 to 3. >> >> Instead .... >> >> 4) In a vertex wise analysis of area (using newer version of >> mris_preproc) what nuisance factors are people using - does it make >> sense to use total brain surface area (rather than say ICV as one >> might use in thickness) and in which case does it make a difference to >> use total pial or white matter area ? >> >> I have read some of the discussions on the forum about this, and some >> of the references posted. I wonder whether someone might tell me >> whether they agree with my thinking. I have 2 groups (controls and a >> patient gp) - I am interested in the global as well as local effects >> of group on my dependent measures (thickness, area, volume) and hence >> have only included age and ICV as nuisance factors in my vertex wise >> analysis - is this reasonble ? - if I was more interested in >> local/regional effects would it be then reasonable to include mean >> hemispheric thickness, mean GM volume, or mean GM/WM area as nuisance >> factors in a vertex wise analysis ... Furthermore, am I right in >> thinking if I was carrying out an ROI based analysis of any of these >> dependent measures then by definition I should include the appropriate >> correction factor to ensure that I am not just seeing a global effect ? > It probably does not make sense to use ICV for surface area. People > sometimes use total surface area, but I think it is an open question (as > is the exact method for correction: nuisance regressor or scaling). But > accounting for the global effect should reveal local effects by > definition. And, yes, you would want to do the same thing for your ROI > analysis. >> >> 5) What do the dependent measures - >> intensity_deep/intensity_superficial, >> intensity_deep.mgz/intensity_superficial.mgz and white K/H measure in >> qdec ... > These are curvature measures. I can't remember what the K and H are. Bruce? >> >> 6) An additional question - I note in the recon-all.log file that >> mris_anatomical_stats is run with the flags "-mgz -cortex ... - what >> are these flags for ? > -mgz just says to look for an mgz file. At one point, we had another > format, but that was years ago; but the -mgz remains. -cortex passes the > cortical label for computing statistics across all of cortex. > > doug > >> >> Thanks. >> >> Mahinda >> >> >> >> On Mon, May 21, 2012 at 8:03 PM, Mahinda Yogarajah >> <y.mahi...@gmail.com <mailto:y.mahi...@gmail.com>> wrote: >> >> Dear Experts, >> >> I have some related questions: >> >> 1) Am I right in thinking that the default settings for recon-all >> produce aparc files where the areas are based on white matter and >> not pia ? >> 2) Therefore am I right in assuming that when I use >> aparcstats2table across my subjects using "--meas area", the area >> is also going to be based on white matter unless I redo the >> processing using mris_anatomical with a "pial" flag >> 3) If the above is correct, why is the default to measure areas >> based on white matter - intuitively this does not make sense to me >> or seem as useful as gray matter ROI areas (particularly as from >> my understanding there are further assumptions made in the >> algorithsm that does the labelling of underlying white matter from >> the cortex) - are their papers where white matter areas are being >> reportted ? >> 4) In a vertex wise analysis of area (using newer version of >> mris_preproc) what nuisance factors are people using - does it >> make sense to use total brain surface area (rather than say ICV as >> one might use in thickness) and in which case does it make a >> difference to use total pial or white matter area ? >> 5) Finally what do the dependent measures - >> intensity_deep/intensity_superficial, >> intensity_deep.mgz/intensity_superficial.mgz and white K/H measure >> in qdec ... >> >> Thanks. >> >> Mahinda >> >> >> >> >> _______________________________________________ >> 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
