Dear Doug, Thank you very much for your advice! We get to extract results for the volumes from a ".curv file encoded ROI" using your recommended command lines (mri_binarize and mri_segstats ), but unfortunately the results are much smaller (around 3 times) than when we extract total gray matter volumes from a respective ".label file encoded ROI" using mris_anatomical_stats .
Example: Volumes from a ".curv file encoded ROI" using your recommended command lines (mri_binarize and mri_segstats): Subject1 = 1090 Subject2 = 1181 Subject3 = 713 Subject4 = 1230 Volumes from a respective ".label file encoded ROI" (mris_anatomical_stats): Subject1 = 3497 Subject2 = 3786 Subject3 = 2268 Subject4 = 3491 Are the volumes extracted from a ".curv file encoded ROI" (using mri_binarize and mri_segstats) an estimation of the total gray matter volumes? Why these values are differing that much? Thank you very much, Josue Dalboni ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: Wednesday, October 5, 2016 5:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Quantifying volumes I would binarize the curv file with mri_binarize --i lh.yourcurvfile --abs --min .0000001 --o lh.yourcurvfilebin.mgh Then compute the volume with mri_segstats --seg lh.yourcurvfilebin.mgh --id 1 --i lh.volume --accumulate --sum lh.vol.yourcurv.sum On 10/05/2016 09:09 AM, Josue Luiz Dalboni Da Rocha wrote: > Dear Douglas, > > I have a ".curv" file that contains the curvature information inside an > automatically delineated ROI and 0 everywhere else. > I would like to calculate the volume of this ROI, > > Can I extract statistics directly from the ".curv" file? > > Best regards, > Josue > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve > <gr...@nmr.mgh.harvard.edu> > Sent: Tuesday, October 4, 2016 9:41 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Quantifying volumes > > What is the nature of the segmentation? Is it just a binary (1=in, > 0=out) segmentation? And what file format? In general we don't use .w > anymore, but it can be converted into something else. > > doug > > > On 10/03/2016 12:35 PM, Josue Luiz Dalboni Da Rocha wrote: >> Dear Douglas, >> >> >> I have a segmented gyrus curvature file (.curv or .w) and I would like >> to calculate the volume (and other statistics) of this gyrus. >> >> >> I currently only know mris_anatomical_stats to perform that, but >> requiring a '.label' file. >> >> >> Can I extract statistics directly from the ".curv" file? >> >> >> Or can I convert directly from .curv to .label in order to extract >> these statistics? >> >> >> As another option, is it feasible to convert the '.curv' file to nifti >> volume (mri_surf2vol), binarize it (mri_binarize), and then convert to >> label (mri_cor2label)? >> >> >> What does the output nifti file from 'mri_surf2vol' contain? Does it >> contain the complete volume behind the surface? Or does it only >> contain the surface over the 3D space? >> >> >> Thank you very much in advance for your help! >> >> >> Best regards, >> >> Josue >> >> >> >> _______________________________________________ >> 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. > > > _______________________________________________ > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
