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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
