Re: [Freesurfer] White matter volume of a costumized Gyrus
You will need to create an annotation with your label in it. This might be tricky to do depending on what you want. The easy way is to run mris_label2annot with only your label, then run mri_aparc2aseg to generate something like the wmparc.mgz (look in the recon-all.log file for the command line that generated wmparc.mgz but specify your annot with --annot). View the label to make sure it is what you want, then run mri_segstats. On 5/9/17 7:23 AM, Josue Luiz Dalboni Da Rocha wrote: Dear Freesurfer team, I am working with calculated volumes of a gyrus (a costumized label). I currently use mris_anatomical_stats to calculate the volumes of my gyrus (in label format). According to the freesurfer tutorial (as I understood), one of the stats outputted from mris_anatomical_stats is the volume of the gray matter surrounding the white/gray matter border (a surface) specified by the inputted label. We are actually interested in the white matter volume (instead of gray matter volume) inside this ROI (a gyrus in our case) specified by the label. I didn't find yet a command in freesurfer from where I can extract the white matter volume of a gyrus from a costumized label. Could someone advise me? Best regards, Josue ___ 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.
Re: [Freesurfer] White matter volume of a costumized Gyrus
Hi Josue how would you define the borders of the white matter of the gyrus? I guess you could use the wmparc stuff and just count voxels based on a distance constraint cheers Bruce On Tue, 9 May 2017, Josue Luiz Dalboni Da Rocha wrote: Dear Freesurfer team, I am working with calculated volumes of a gyrus (a costumized label). I currently use mris_anatomical_stats to calculate the volumes of my gyrus (in label format). According to the freesurfer tutorial (as I understood), one of the stats outputted from mris_anatomical_stats is the volume of the gray matter surrounding the white/gray matter border (a surface) specified by the inputted label. We are actually interested in the white matter volume (instead of gray matter volume) inside this ROI (a gyrus in our case) specified by the label. I didn't find yet a command in freesurfer from where I can extract the white matter volume of a gyrus from a costumized label. Could someone advise me? Best regards, Josue ___ 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] White matter volume of a costumized Gyrus
Dear Freesurfer team, I am working with calculated volumes of a gyrus (a costumized label). I currently use mris_anatomical_stats to calculate the volumes of my gyrus (in label format). According to the freesurfer tutorial (as I understood), one of the stats outputted from mris_anatomical_stats is the volume of the gray matter surrounding the white/gray matter border (a surface) specified by the inputted label. We are actually interested in the white matter volume (instead of gray matter volume) inside this ROI (a gyrus in our case) specified by the label. I didn't find yet a command in freesurfer from where I can extract the white matter volume of a gyrus from a costumized label. Could someone advise me? Best regards, Josue ___ 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.
