Hi Bruce, I have followed your suggestions using the 'custom fill' botton and then saving the label and using mri_label2vol. This is the command I used:
mri_label2vol --label gyrif_lh.label --temp MNI152_T1_1mm_brain.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --o gyrif_lh.nii.gz However, the nifti file looks like this (see attached) What am I doing wrong? Thank you for your help! Angela > Hi Angela > > in tksurfer you can show the overlay, and use the "custom fill" button to > fill the area that is above threshold on the surface. Then save it as a > label and use mri_label2vol to write it into a volume. If the output > volume > you give has the extension .nii.gz it will save it in nifti for you > > cheers > Bruce > > > > On Sun, 2 Nov 2014, angela.fav...@unipd.it wrote: > >> Dear all, >> I found some interesting findings about gyrification and I would like to >> test any related problem in structural connectivity. >> My idea was to use the area where I found significant lower gyrification >> in my sample to perform probabilistic tracking with FSL. >> My question is: is there any way to label the area of significant >> difference (or I have to manually draw it) and to transform it in a >> nifti >> format? >> >> Angela >> >> >> >> >> >> _______________________________________________ >> 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. > > >
_______________________________________________ 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.
