Thanks! so this is the command I've used: mri_aparc2aseg --annot freeSurfer_lobes --s P2 --o freeSurfer_Results/P2/labels/freeSurfer_lobes.nii.gz
a couple of question I have now: 1. what lables (numbers) correspond to the 5 main lobes? looking at the "FreeSurferColorLUT.txt", I'm assuming the lables I'm interested in are in the range of 1000-1035 (left) and 2000-2035 (right), is this correct? should I now manually add the relevant sections to get the 5 lobes?! or is there an automated way to do this?! 2. also, with "mri_label2vol" I was using the registration flags to move the labels into the native subject space, but this way (using mri_aparc2aseg) I get the labels in the freeSurfer space! are there options to move the lables? or should I do it as a separate step? if so, could you please tell me which command I should use? sorry for bugging you with so many questions! -M On 11/21/2013 01:42 PM, Douglas N Greve wrote: > use mri_aparc2aseg instead of label2vol. This is how aparc+aseg.mgz is > created. Look in the recon-all.log file for the command line used. > > doug > > > On 11/21/2013 10:44 AM, Mojdeh Zamyadi wrote: >> Hi all, >> >> I want to convert the cortical labels I get in freeSurfer to volumetric >> ROIs in the subject space and I've followed the steps mentioned in: >> http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/ >> >> except since I'm interested in lobe mapping I've changed the first >> commands, more specifically these are the different command I've run: >> >> 1. mri_annotation2label --subject P2 --hemi lh --outdir >> freeSurfer_Results/P2/labels/ --lobesStrict >> freeSurfer_Results/P2/labels/freeSurfer_lobes >> >> 2. mri_annotation2label --hemi lh --subject P2 --outdir >> freeSurfer_Results/P2/labels/ --annotation >> freeSurfer_Results/P2/labels/lh.freeSurfer_lobes.annot >> >> 3. tkregister2 --mov freeSurfer_Results/P2/mri/rawavg.mgz --noedit --s >> P2 --regheader --reg freeSurfer_Results/P2/register.dat >> >> 4. mri_label2vol --label freeSurfer_Results/P2/labels/lh.parietal.label >> --temp freeSurfer_Results/P2/mri/rawavg.mgz --subject P2 --hemi lh --o >> freeSurfer_Results/P2/labels/lh.parietal.nii.gz --proj frac 0 1 .1 >> --fillthresh 1 --reg freeSurfer_Results/P2/register.dat >> >> the issue I have now is that the final ROI I get (e.g. >> "lh.parietal.nii.gz") looks like a series of disconnected points! I was >> wondering how I can get a smooth (i.e. filled) volumetric ROI? >> >> Thanks, >> -Mojdeh >> >> _______________________________________________ >> 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.
