Hi Bruce, Yes, the one from label2vol "just hugs the white boundary" Doug, I will try with the --proj frac 0 1 .1 option and let you all know. Thanks Mehul
On Wed, Jun 26, 2013 at 3:58 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > Oh, right. Mehul, you'll need to tell it to fill the ribbon with > something like --proj frac 0 1 .1 > doug > > On 06/26/2013 06:55 PM, Bruce Fischl wrote: > > won't the anatomical_stats one multiply thickness by surface area, > > where the label2vol will only fill voxels on the gray/white boundary, > > not all the way through the ribbon? Mehul: if you visualize the one > > from label2vol does it fill the ribbon or just hug the white boundary? > > > > On Wed, 26 Jun 2013, Douglas N Greve wrote: > > > >> not necessarily. That is a very small structure, and getting a few edge > >> voxels wrong will mess things up a lot. Can you load lh-new-erc.mgz in > >> tkmedit and load the surfaces too and see how good it did? > >> doug > >> > >> On 06/26/2013 06:49 PM, Mehul Sampat wrote: > >>> Hi Folks, > >>> > >>> > >>> I am trying to create an entorhinal cortex volume from > >>> ?h.entorhinal_exvivo.label using mri_label2vol > >>> > >>> > >>> I cd to the subject dir ($SUBJECTS_DIR/bert) and the command I use is: > >>> > >>> > >>> *mri_label2vol --label label/lh.entorhinal_exvivo.label --temp > > mri/nu.mgz --identity --o mri/lh-new-erc.mgz* > >>> > >>> > >>> > >>> > >>> > >>> I took the sum of the voxels in this new mask i created > >>> (lh-new-erc.mgz) and it is 215; > >>> I looked at the volume provided inlh.entorhinal_exvivo.stats and it > >>> is 925; (from the log file I believe this is created using the command: > >>> > >>> > >>> mris_anatomical_stats -mgz -f ../stats/lh.entorhinal_exvivo.stats -b > >>> -l ./lh.entorhinal_exvivo.label bert lh white) > >>> > >>> > >>> > >>> > >>> > >>> I was expecting the numbers to match orat-leastbe close; I am > >>> guessing I am using mri_label2vol incorrectly ? > >>> > >>> > >>> Could someone help me with this issue ? > >>> > >>> > >>> Thanks > >>> > >>> > >>> Mehul > >>> > >>> > >>> > >>> > >>> > >>> > >>> _______________________________________________ > >>> 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 > > > 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. > >
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