check out this page http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
On 09/15/2015 06:02 PM, Jinsong Tang wrote: > Hello Douglas, > > I think there maybe somthing wrong in this step. (Ｉwant to create a > VOI in native space) > mri_convert -rl rawavg.mgz -rt nearest aparc+aseg.mgz > aparc+aseg2raw.nii.gz > > aparc+aseg.mgz file has 1035, while aparc+aseg2raw.nii.gz does not > have 1035. > > Following your suggestions using mri_binarize. > mri_binarize --match 1035 --i aparc+aseg.mgz --o l_ins_fs_avg01.mgz > mri_convert -rl rawavg.mgz -rt nearest l_ins_fs_avg01.mgz > l_ins_fs_rawavg01.nii.gz > > This works. But the intensity value from l_ins_fs_rawavg01.nii.gz “ > -32768 or 32768 ” instead of "0 or 1". > > So I think maybe mir_convert have change the values. How to keep the > value unchanged? > > Thanks, > > Jinsong > > > > On Tue, Sep 15, 2015 at 2:39 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > I think you've done somthing wrong. If there is no 1035, then nothing > should work. It may be that you should use thresholds of 1034.5 and > 1035.5. Also you can use mri_binarize --match 1035 instead of > fslmaths. > That will work on any data format. > > On 09/14/2015 06:47 PM, Jinsong Tang wrote: > > Hello, > > > > I want to use FreeSurfer to create subject specific ROI for left > > insua. The lable number is 1035. > > > > I use： > > mri_convert -rl rawavg.mgz -rt nearest aparc+aseg.mgz > > aparc+aseg2raw.nii.gz > > fslmaths aparc+aseg2raw.nii.gz -uthr 1035 -thr 1035 > l_ins_fs_rawavg.nii.gz > > > > I found the label is different bewteen aparc+aseg2raw.nii.gz and > > aparc+aseg.mgz. > > Lable number 1035 can not be found in aparc+aseg.mgz. so there is no > > ROI was created. > > > > Then I use: > > > > mri_convert aparc+aseg.mgz aparc+aseg.nii.gz > > fslmaths aparc+aseg.nii.gz -uthr 1035 -thr 1035 l_ins_fs_avg.nii.gz > > mri_convert -rl rawavg.mgz -rt nearest l_ins_fs_avg.nii.gz > > l_ins_fs_rawavg.nii.gz > > > > Is this correct? > > > > Thanks, > > > > Jinsong > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <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. > > > > > -- > Jinsong Tang, MD > Institute of Mental Health > The Second Xiangya Hospital , Central South University > 139 Renmin Road, Changsha Hunan 410011, P.R. China > > > _______________________________________________ > 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
