label2surf is an FSL command, so you can get a more authoritative answer on the FSL list, but I'd try one of the files in the surf/ directory, like lh.white or rh.white.
On Fri, 27 Sep 2013, std...@virgilio.it wrote:
Hi list and Anastasia. Thank you very much. mri_annotatiion2label works fine. Becouse I should run this command: label2surf -s <surface> -o <outputsurface> -l <labels> -s,--surf input surface -o,--out output surface -l,--labels ascii list of label files I should provide also surface file relatively to each .label previously created with mri_annotatiion2label. How can I do? Thanks, Stefano ----Messaggio originale---- Da: ayend...@nmr.mgh.harvard.edu Data: 26-set-2013 0.57 A: <std...@virgilio.it> Cc: <freesurfer@nmr.mgh.harvard.edu> Ogg: Re: R: Re: [Freesurfer] Import FS data to FSL Try mri_annotation2label. On Wed, 25 Sep 2013, std...@virgilio.it wrote: > For FSL guide: > > I should transforms a group of labels into a surface > > Usage: > > label2surf -s <surface> -o <outputsurface> -l <labels> > > Compulsory arguments (You MUST set one or more of): > > -s,--surf input surface > > -o,--out output surface > > -l,--labels ascii list of label files > > Optional arguments (You may optionally specify one or more of): > > -v,--verbose switch on diagnostic messages > > -h,--help display this message > > > but I should create a lh/rh.frontal.label and use it for label2surf. > > With mdi_binarize I can create .nii.gz but no .label. Is that correct? > > How I can do it? > > > Thanks, > > > Stefano > > > > > ----Messaggio originale---- > Da: ayend...@nmr.mgh.harvard.edu > Data: 25-set-2013 17.49 > A: <std...@virgilio.it> > Cc: <freesurfer@nmr.mgh.harvard.edu> > Ogg: Re: [Freesurfer] Import FS data to FSL > > > 1 - Yes. > 2 - You can use mri_aparc2aseg to grow the cortical labels into the white > matter (say, by 2mm). The file that it will produce will be a volume file, > so then you just run mri_binarize to extract specific labels. Make sure > you save them in nifti format for FSL. > > On Wed, 25 Sep 2013, std...@virgilio.it wrote: > > > Hi list, > > > > I have 2 questions, please. > > > > 1-The bedpostX that I have run for TRACULA could be used for PROBTRACKX > > (FSL)? > > > > 2-I'd like to export cortical masks from FS to FSL. > > > > An option is mri_binarize but this way failed in probtrackx (fsl). > > FSL list have advised me that I should use label2surf command to convert > > label to surface files. > > > > Where could find the .label (according to FreeSurferColorLUT.txt) to build > > mask of frontal, parietal, motor, sensor, temporal and occipital lobes? > > > > Do you have other ways that you advise me? > > > > > > Thanks, > > > > > > Stefano > > > > > > > > > > > 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. > > > > >
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