Anastasia thank you very much! I have wrote to FSL mail list. They have uploaded a new web page of FDT. Anyway, these are the commands: mris_convert lh.white lh.white.giiecho lh.BA44.label lh.BA45.label > listOfAreas.txt label2surf -s lh.white.gii -o lh.BA44.gii -l listOfAreas.txtStefano
----Messaggio originale---- Da: ayend...@nmr.mgh.harvard.edu Data: 27-set-2013 16.44 A: <std...@virgilio.it> Cc: <freesurfer@nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] R: Re: R: Re: Import FS data to FSL 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. > > > > > > > > > > > > >_______________________________________________ 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.
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