mri_label2vol will take segmentations as an input look at the --help doug
On 02/15/2013 04:25 PM, Roderick McColl wrote: > Sorry for the bother, but there isn't a label for L or R WM. > Should I use mri_vol2vol on the aseg.mgz file and the mni152.register.dat > file instead i.e. just register aseg.mgz into MNI152 space? > Not sure how to make this use a nearest neighbor interpolation though. > Thanks > -roddy > > -----Original Message----- > From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Sent: Friday, February 15, 2013 3:04 PM > To: Roderick McColl > Subject: Re: Convert aseg.mgz to .nii and into MNI space with FSL dimensions > > In that case, use mri_label2vol with the following reg > $FREESURFER_HOME/average/mni152.register.dat > doug > > On 02/14/2013 11:02 AM, Roderick McColl wrote: >> Thanks very much. >> I should have made myself clearer. >> I would like to use $FREESURFER_HOME/subjects/fsaverage/mr/aseg.mgz >> for some analysis in MNI512 (FSL) space. >> So should I use mni152reg on the orig.mgz file in that folder to generate >> the transform? >> -roddy >> >> ________________________________________ >> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] >> Sent: Wednesday, February 13, 2013 4:48 PM >> To: Roderick McColl >> Cc: 'Clark Fisher'; freesurfer@nmr.mgh.harvard.edu >> Subject: Re: Convert aseg.mgz to .nii and into MNI space with FSL >> dimensions >> >> you can use mni152reg to compute the registration to the MNI152 space. >> Make sure to spec the 1mm target. You can then use mri_label2vol to >> map aseg.mgz to the MNI152 space. >> >> doug >> >> On 02/13/2013 03:40 PM, Roderick McColl wrote: >>> Hello all, >>> I have a need to generate LH and RH WM masks for analysis. >>> I can convert aseg.mgz to aseg.nii but the dims are 256x256x256 and I >>> need to use the FSL MNI format which is 182x218x182. >>> Is there a recipe for cropping / translating etc to match the >>> aseg.mgz atlas with the FSL atlases? >>> Thanks >>> -roddy >>> >>> --------------------------------------------------------------------- >>> --- >>> >>> UT Southwestern Medical Center >>> The future of medicine, today. >> -- >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> >> 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. >> >> >> >> > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > -- 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: 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
