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 <[email protected]> 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 > [email protected] > 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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