Hi! Ok! That would be a good improvement :)
Thanks to both! Cheers, Andreia Citando Douglas N Greve <gr...@nmr.mgh.harvard.edu>: > Actually, you are right! Most of the non-gray matter structures in the > medial wall are zeroed out, but the part that goes through the hippo and > amygdala are non-zero. As Mike points out, this is going to be a very > small portion of the total cortical volume, but we'll find a way to > remove it. > doug > > _andre...@sapo.pt wrote: >> Hi Michael and Doug, >> >> Michael: >> "As you noted, the surfaces bisect the hippocampus and amygdala, so the >> small amount of tissue outside the pial surface is not included in the >> surface based measures of total GM volume. Compared to the overall >> variation in brain size, this should be inconsequential. >> >> cheers, >> -MH" >> >> I got a little confused with your answer. The calculation is >> everything inside the pial surface - everything inside the wm surface. >> What is outside is half hippocampus/amygdala and is not included, ok. >> But the other halves are inside the surfaces, being then included, right? >> >> Doug: >> >> If the thickness was 0 in those areas that would make sense. But do >> the surfaces "have" the information that in those regions the >> structures are hippocampus and amygdala? >> >> I checked if the thickness was 0 and from what I'm understanding it is >> 5mm. What I did was to open tkmedit with aparc+aseg and open tksurfer >> (for both hemispheres). Then, I used the buttons "Save point" and "Go >> to saved point" to go from tkmedit to tksurfer. What happened was that >> when the point was located in the hippocampus or amygdala in tkmedit >> it had a correspondence in tksurfer in regions which have a thickness >> value. >> >> Please see figures in attachement (green arrows are amygdala poinst >> and blue arrows are hippocampus points) >> >> Am I missing something? >> >> Thank you, >> Andreia >> >> >> >> >> Citando Douglas N Greve <gr...@nmr.mgh.harvard.edu>: >> >>> Hi Andreia, I don't think this is a problem for the GM volume (ie, parts >>> of the amyg or hippo getting counted twice). The thickness should be 0 >>> in those areas, so they should not contribute to GM volume. The >>> computation of the WM volume is done in a different way (still surface >>> based) but automatically excludes subcortical structures. >>> doug >>> >>> _andre...@sapo.pt wrote: >>>> Hello, >>>> >>>> Recalling these emails: >>>> >>>> "The methods are somewhat different. For the value in the aseg.stats >>>> table, the method is to compute the total volume inside the pial >>>> surface >>>> and subtract the total volume inside the white surface. For >>>> mris_anatomical_stats, the method is to compute the thickness times >>>> area >>>> of each vertex. This method will probably underestimate the total >>>> volume >>>> because it uses the area of the white surface when it should use the >>>> area of the surface in the middle between the white and pial surfaces. >>>> I've added this to the list of known issues on our release page. >>>> >>>> doug >>>> >>>> Alexopoulos, Dimitrios wrote: >>>> >>>>> I have generated surfaces using the the centos4 build (version 5.0) >>>>> and want to confirm that my surface-based GM and WM volumes are >>>>> correct. >>>>> For the surface-based GM calculation I originally used >>>>> 'mris_anatomical_stats -l lh.cortex.label subjectID hemi' >>>>> (run from within the 'label' subdirectory) and for WM i used >>>>> 'mris_wm_volume subjectID hemi' (run from within >>>>> the 'surf' subdirectory). >>>>> When I add the calculated left/right cortical volumes, I get a total >>>>> that is different from what is output in >>>>> the 'aseg.stats' file, which in version 5.0 is noted to contain >>>>> total surface-based GM volume >>>>> (Cortex, CortexVol: Total cortical gray matter volume (based on >>>>> surface-stream). >>>>> What are the correct GM and WM surface-based volumes? >>>>> Thanks. Jim" >>>>> >>>> >>>> >>>> I question came up to me: >>>> >>>> The surfaces in the hippocampus/amygdala are inaccurate and should be >>>> ignored. However, in version 5.0 the cortical volume is surface-based, >>>> thus it takes into account the surfaces in the hippocampus/amygdala, >>>> is this correct? >>>> >>>> If so, it is expected that an error is introduced in the surface-based >>>> calculation of cortical volume. Has anyone checked the influence of >>>> this error? Or FS compensates for the inaccuracy of the surface >>>> estimation of these regions somehow? >>>> >>>> Thanks! >>>> >>>> Andreia >>>> >>>> _______________________________________________ >>>> 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. >>> >>> >> >> >> ------------------------------------------------------------------------ >> >> >> ------------------------------------------------------------------------ >> > > -- > 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 > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
