Hi Hong Xin, Yes. fslview will complain. After you install freesurfer. You can use freeview to display my parcellation and the fsl template. You should verify that they align perfectly well. So my parcellation and FSL mni template are in alignment, but the header information are not the same.
Since the parcellations are released as part of freesurfer, I am cc-ing the freesurfer list so other users might benefit from your question. Cheers, Thomas On Sun, Aug 23, 2015 at 10:30 AM, Hong Xin (SBIC) <hong_...@sbic.a-star.edu.sg> wrote: > Thanks you very much for the quick response. We use FSL for processing, which > displays the parcellations and template/our images in different orientations > and we were not able to overlay them due to the different matrix size. I'll > install freesurfer and try mri_vol2vol. > Thanks again. > > ________________________________________ > From: Thomas Yeo [thomas....@nus.edu.sg] > Sent: Friday, August 21, 2015 5:36 PM > To: Hong Xin (SBIC) > Subject: Re: question on Cortical Parcellation Estimated by Intrinsic > Functional Connectivity > > Hi Xin, > > Actually, the 256x256x256 and 182x218x182 volumes are already in > alignment. It's just that their header information are different. > Therefore you do not need to perform an image registration. I suggest > you use mri_vol2vol, which is a freesurfer function: > > mri_vol2vol --mov my256x256x256_parcellation.nii.gz --targ > 182x182x182_brain.nii.gz --o output.nii.gz --regheader --interp > nearest > > The above command should work. Let me know if you have other issues. > > Cheers, > Thomas > > On Fri, Aug 21, 2015 at 5:32 PM, Hong Xin (SBIC) > <hong_...@sbic.a-star.edu.sg> wrote: >> Hi Prof Yeo, >> >> >> >> We would like to apply the cortical parcellations to our study. Our images >> are in the MNI space (matrix size 182x218x182), though the 'parcellations in >> Nonlinear MNI152 Volume Space' match the MNI template (MNI152_T1_1mm_brain), >> the labeled image has a different matrix size (256x256x256) and orientation. >> Since we are not familiar with freesurfer, we wondered if there is a version >> of the parcellations in the MNI space (with same matrix size and >> orientation) available? Or we need to make it by ourselves? If so, could you >> help to check if the following proposed steps are correct: 1. run a rigid >> body transformation, bring FSL_MNI152_FreeSurferConformed_1mm to >> MNI152_T1_1mm_brain. 2. apply the transformation to the labeled images (eg, >> Yeo2011_7Networks_MNI152_FreeSurferConformed1mm). >> >> >> >> Your input is highly appreciated. >> >> >> >> Best, >> >> Xin > > ________________________________ > > Important: This email is confidential and may be privileged. If you are not > the intended recipient, please delete it and notify us immediately; you > should not copy or use it for any purpose, nor disclose its contents to any > other person. Thank you. _______________________________________________ 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.
