[Freesurfer] Desikan Killiany Atlas measurements
Dear all, I want to get the measurements of meancurvature, thickness, white matter volume and gray matter volume based on Desikan-Killiay Atlas. I would like to learn whether the commands I used to get them are the correct ones (in terms of content) & for Desikan Killiany atlas? *For meancurv: * aparcstats2table --hemi lh --subjects S1 S2 S3 --parc aparc --meas meancurv -t lh.parc.meancurv.txt *For thickness:* aparcstats2table --hemi rh --subjects S1 S2 S3 --parc aparc --meas meancurv -t rh.parc.meancurv.txt *For WM volume:* asegstats2table --all-segs --subjects S1 S2 S3 \-t table.wmparc.txt -d space --stats wmparc.stats *For GM volume:* aparcstats2table --subjects S1 S2 S3 --hemi lh --meas volume --parc=aparc --tablefile aparc_lh_volume_table.txt Thanks in advance, ___ 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.
Re: [Freesurfer] Desikan Killiany Atlas measurements
mostly right, a few corrections below On 05/21/2014 10:35 AM, Buse Merve Ürgen wrote: > Dear all, > I want to get the measurements of meancurvature, thickness, white > matter volume and gray matter volume based on Desikan-Killiay Atlas. > I would like to learn whether the commands I used to get them are the > correct ones (in terms of content) & for Desikan Killiany atlas? > > *For meancurv: * > aparcstats2table --hemi lh --subjects S1 S2 S3 --parc aparc --meas > meancurv -t lh.parc.meancurv.txt --parc=aparc > > *For thickness:* > aparcstats2table --hemi rh --subjects S1 S2 S3 --parc aparc --meas > meancurv -t rh.parc.meancurv.txt Use--parc=aparc --meas thickness -t rh.parc.thickness.txt > > *For WM volume:* > asegstats2table --all-segs --subjects S1 S2 S3 \-t table.wmparc.txt -d > space --stats wmparc.stats > > *For GM volume:* > aparcstats2table --subjects S1 S2 S3 --hemi lh --meas > volume--parc=aparc --tablefile aparc_lh_volume_table.txt > > Thanks in advance, > > > > ___ > 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.
Re: [Freesurfer] Desikan Killiany Atlas measurements
Thank you so much! Can I also learn what is the difference between the gray matter values in lh.aparc.stats file and the gray matter values from the command below; >> aparcstats2table --subjects S1 S2 S3 --hemi lh --meas >> volume--parc=aparc --tablefile aparc_lh_volume_table.txt > Thanks, -- 21 May 2014 tarihinde 18:19 saatinde, Douglas N Greve şunları yazdı: > > mostly right, a few corrections below > >> On 05/21/2014 10:35 AM, Buse Merve Ürgen wrote: >> Dear all, >> I want to get the measurements of meancurvature, thickness, white >> matter volume and gray matter volume based on Desikan-Killiay Atlas. >> I would like to learn whether the commands I used to get them are the >> correct ones (in terms of content) & for Desikan Killiany atlas? >> >> *For meancurv: * >> aparcstats2table --hemi lh --subjects S1 S2 S3 --parc aparc --meas >> meancurv -t lh.parc.meancurv.txt > --parc=aparc >> >> *For thickness:* >> aparcstats2table --hemi rh --subjects S1 S2 S3 --parc aparc --meas >> meancurv -t rh.parc.meancurv.txt > Use--parc=aparc --meas thickness -t rh.parc.thickness.txt >> >> *For WM volume:* >> asegstats2table --all-segs --subjects S1 S2 S3 \-t table.wmparc.txt -d >> space --stats wmparc.stats >> >> *For GM volume:* >> aparcstats2table --subjects S1 S2 S3 --hemi lh --meas >> volume--parc=aparc --tablefile aparc_lh_volume_table.txt >> >> Thanks in advance, >> >> >> >> ___ >> 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
Re: [Freesurfer] Desikan Killiany Atlas measurements
aparc.stats has all of the values (eg, thickness, area, volume, curv) for each ROI for a single subject. When you run aparcstats2table, you extract one of those for each subject for all ROIs and put them into a single table file On 05/21/2014 01:21 PM, Buse Merve Urgen wrote: > Thank you so much! Can I also learn what is the difference between the gray > matter values in lh.aparc.stats file and the gray matter values from the > command below; >>> aparcstats2table --subjects S1 S2 S3 --hemi lh --meas >>> volume--parc=aparc --tablefile aparc_lh_volume_table.txt > Thanks, > -- > > 21 May 2014 tarihinde 18:19 saatinde, Douglas N Greve > şunları yazdı: > >> mostly right, a few corrections below >> >>> On 05/21/2014 10:35 AM, Buse Merve Ürgen wrote: >>> Dear all, >>> I want to get the measurements of meancurvature, thickness, white >>> matter volume and gray matter volume based on Desikan-Killiay Atlas. >>> I would like to learn whether the commands I used to get them are the >>> correct ones (in terms of content) & for Desikan Killiany atlas? >>> >>> *For meancurv: * >>> aparcstats2table --hemi lh --subjects S1 S2 S3 --parc aparc --meas >>> meancurv -t lh.parc.meancurv.txt >> --parc=aparc >>> *For thickness:* >>> aparcstats2table --hemi rh --subjects S1 S2 S3 --parc aparc --meas >>> meancurv -t rh.parc.meancurv.txt >> Use--parc=aparc --meas thickness -t rh.parc.thickness.txt >>> *For WM volume:* >>> asegstats2table --all-segs --subjects S1 S2 S3 \-t table.wmparc.txt -d >>> space --stats wmparc.stats >>> >>> *For GM volume:* >>> aparcstats2table --subjects S1 S2 S3 --hemi lh --meas >>> volume--parc=aparc --tablefile aparc_lh_volume_table.txt >>> >>> Thanks in advance, >>> >>> >>> >>> ___ >>> 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
