You can use --proj frac 0 1 .1 See the --help for more info doug On 11/29/14 8:22 PM, Bruce Fischl wrote: > 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 > >
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