Hi Dr. Fischl and Dr. Greve, So moving the mouse over the medial wall seems to have all vertices within that to have a zero mm thickness as expected. The yellow outline is the lh.cortex.label and it seems to look good to me i.e. majority of the medial wall is properly masked. To be noted, this was the subject with 53 vertices labeled as 0s, which as you mentioned should be a substantial number. I am wondering what could be causing this?
Lastly, I was wondering for cortical thickness analysis, is there a method to ensure the same number of vertices across all subjects with a corresponding mm thickness value. I have yet to try some commands, but preemptively I think if using mri_label2label with the trglabel lh.cortex.label as found in fsaverage directory and for each subject map their lh.cortex.label to fsaverage's lh.cortex.label and then from here I know I can run mris_anatomical_stats to extract average thickness, is there a command maybe using mris_convert with the label option to convert the label to the white surface and then using mris_convert with a -c option to have the scalar mm values corresponding to each vertex? or is this not a recommended approach? I would like ultimately import this into MATLAB to do some statistics and then view in freeview as a scalar overlay. Please advise. Thanks for the help, Taha On Tue, Oct 18, 2016 at 7:49 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Taha > > none that I can think of. The medial wall is pretty substantial region > though - I am more concerned about your subject with only 53 vertices in > it. You can visualize it by loading the ?h.cortex.label onto the inflated > surface. Everything not in the label should be set to 0 > > cheers > Bruce > > > > On Tue, 18 Oct 2016, Taha Abdullah wrote: > > I see now, thanks for the answer. If I may, is there any particular reason >> why such a disparity between >> two subjects, is this due to anatomical variability between individuals? >> I was surprised by the 9,000 >> values that was missing. >> >> On Fri, Oct 14, 2016 at 10:40 AM, Douglas Greve < >> gr...@nmr.mgh.harvard.edu> wrote: >> >> The entire medial wall has thickness values of 0 because there is >> no cortex there. There >> needs to be a surface in that area because we need a closed surface. >> >> >> On 10/12/16 8:10 PM, Taha Abdullah wrote: >> Hello All, >> Quick question, I ran recon-all with the qcache option and after >> converting the >> ?.thickness.fsaverage.mgh to an ascii text file via mri_convert I am >> noticing some vertices >> have 0mm thickness and it varies, for example, one subject had 53 >> vertices labeled as zeros >> while another had over 9,000 vertices. Is there a method I can use to >> have a thickness value >> for each of the 163000+ vertices? I am not sure if this is a possible >> registration issue to >> mni305. >> >> Thanks in advance, >> Taha >> -- >> Taha Abdullah >> Department of Physiology, >> Northwestern University Feinberg School of Medicine >> MS in Physiology and Biophysics, Georgetown University 2015 >> Work Cell: (312)-451-8468 >> >> >> _______________________________________________ >> 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. >> >> >> >> >> -- >> Taha Abdullah >> Department of Physiology, >> Northwestern University Feinberg School of Medicine >> MS in Physiology and Biophysics, Georgetown University 2015 >> Work Cell: (312)-451-8468 >> >> > _______________________________________________ > 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. > > -- *Taha Abdullah* *Department of Physiology,* *Northwestern University Feinberg School of Medicine* *MS in Physiology and Biophysics, Georgetown University 2015* *Work Cell: (312)-451-8468*
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