To add to what Thomas said, I would use mri_label2vol whenever transferring segmentations or labels. In this case, probably it won't make much difference.
doug On 01/27/2014 05:49 AM, Thomas Yeo wrote: > Hi Sooyun, > > To convert the Choi's parcellation to the MNI152 template from FSL, > you should just use mri_vol2vol, rather than FIRST. The command is as > follows:"mri_vol2vol--mov original_choi_MNI152_parcellation.nii.gz > --targ $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz --regheader > --o FSL_choi_MNI152_parcellation.nii.gz --no-save-reg --interp nearest" > > Please note the use of the "--regheader" flag. The Choi volume is in > exactly the SAME space as the > $FSLDIR/data/standard/MNI152_T1_2mm_brain.nii.gz, it's just that the > header information is different. Therefore the "regheader" flag takes > care of that. > > Cheers, > Thomas > > > On Mon, Jan 27, 2014 at 4:31 PM, 조수연 <syduam2...@kaist.ac.kr > <mailto:syduam2...@kaist.ac.kr>> wrote: > > Hello, > > I'm a FreeSurfer beginner and would like to ask a question about > Choi's stratium parcellations. I was doing a research to > incoorporate the parcellations by Choi on my subjects' images to > delve further to understand the distincitve characteristics of > each parcels. I decided to use the > Choi2012_7Networks_MNI152_FreeSurferConformed1mm_LooseMask.nii.gz. > Since my images were on the standardized model from FSL, I > transformed Choi's image to the MNI standard using FIRST of FSL. > Since both images were now on the same MNI space, I viewed both of > them on FSL to make sure that the Loose mask covered my image > completely, but found that the tail bit of my image was a couple > of pixels too longer than Choi's Loosened mask. Do you think there > is a way that I can further "loosen" up Choi's image to fit my > image? Or can you recommend me a different solution to this problem? > > I'll wait for your reply. Thanks! > > Sincerely, Sooyun Cho. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
