Sorry, what is the difference between total and aparc? On 03/24/2014 01:29 PM, _andre...@sapo.pt wrote: > I was also referring to the surface area and thickness (looking at the > files originated from white matter, which is also the default for > aparc I think): > > For surface area > aparc= 72998.7 > total= 72999 > cortex=78090 > > For CT > aparc= 2.422 > total= 2.422 > cortex= 2.313 > > > And also, which volume measure should I use to get total hemisphere > gray volume? > Aseg lhCortexVol=196557.55 (is the surface-based estimation?) > Aparc (the sum of all labels)=199854 > total.stats=199857 > cortex= 204048 > > It seems that the value from total.stats is more approximated to the > one from the sum of aparc. > > I'm using F.S. 5.0. > > Andreia > > > Quoting Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > >> Is this the difference you mean? >> >> [t:D:mri-> grep Cortex ~/tmp/lh.total.stats >> # Measure Cortex, NumVert, Number of Vertices, 118847, unitless >> # Measure Cortex, SurfArea, Surface Area, 78090, mm^2 >> >> [t:D:mri-> grep Cortex ~/tmp/lh.aparc.stats >> # Measure Cortex, NumVert, Number of Vertices, 111237, unitless >> # Measure Cortex, SurfArea, Surface Area, 72998.7, mm^2 >> >> If so this is just the difference in the vertices coverted by >> cortex.label vs aparc >> >> >> >> >> On 03/24/2014 12:49 PM, _andre...@sapo.pt wrote: >>> Hi Doug, >>> >>> I've attached the files. To contextualize a little bit, I'm using >>> Brodmann Areas measures (CT, surface area and volume, thresholded to >>> the correct probability) and I'll be extracting the surface area using >>> pial and white surface. However, I'll be also analyzing whole brain >>> using the aparc stats (again, CT, surface area and volume) - should I >>> use the file that is in agreement with aparc? >>> >>> I don't understand why total.stats gives different values from >>> cortex.stats since I've created the total.stats file using the command: >>> >>> mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total.stats -b >>> SUBJ lh white >>> >>> >>> >>> One more question: is the ?hCortexvol value from aseg that I should >>> use to get the total volume of each hemisphere? >>> >>> Sorry for so many questions... >>> >>> Thank you! >>> >>> Andreia >>> >>> >>> Quoting Douglas Greve <gr...@nmr.mgh.harvard.edu>: >>> >>>> How much of a difference is there? There should not be much, but there >>>> will be some because the aparc does not cover the exact same vertices as >>>> cortex.label >>>> doug >>>> >>>> >>>> >>>> On 3/24/14 8:04 AM, _andre...@sapo.pt wrote: >>>>> Hello list, >>>>> >>>>> I have a question regarding what stats are more correct to use to get >>>>> whole hemisphere surface area and mean thickness. >>>>> >>>>> The cortex.label values extracted using the two bottom command lines >>>>> don't match aparc stats, however they match in the number of vertices >>>>> between them, and using pial or white surface also results in values >>>>> that make sense comparing each one (higher surface area using pial, >>>>> same thickness, same volumes). >>>>> >>>>> In the past I've been using the two first command lines (in which >>>>> values agree in the same way as cortex.label between them but are also >>>>> in agreement with aparc.stats), however now I'm having this question: >>>>> which one is the correct one to use? >>>>> >>>>> And why does this difference exists? >>>>> >>>>> >>>>> mris_anatomical_stats -l ../label/lh.cortex.label -f lh.total.stats -b >>>>> SUBJ lh white (matches aparcstats) >>>>> >>>>> mris_anatomical_stats -l ../label/lh.cortex.label -f >>>>> lh.total_pial.stats -b SUBJ lh pial (matches aparcstats) >>>>> >>>>> >>>>> mris_anatomical_stats -mgz -f ../stats/lh.cortex_pial.stats SUBJ lh >>>>> pial (does not match aparcstats) >>>>> >>>>> mris_anatomical_stats -mgz -f ../stats/lh.cortex_white.stats SUBJ lh >>>>> white (does not match aparcstats) >>>>> >>>>> >>>>> Thank you in advance, >>>>> Andreia >>>>> _______________________________________________ >>>>> 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. >>> >> -- >> 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: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> _______________________________________________ >> 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 > >
-- 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
