Hi Angela that actually looks ok. It should follow the gray/white boundary I believe. Have you looked at it in the individual subject space without mapping it to the MNI coords? I think there are options in mri_label2vol to fill in the whole cortical ribbon instead of just painting the gray/white boundary but Doug can give you the details after the holiday weekend is over
On Sat, 29 Nov 2014, angela.fav...@unipd.it wrote: > 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
