I have tried several thing like opening on MriCroN and tkregister as: tkregister2 --mov /root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --targ /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz --reg /root/trabajo/freesurfer/subjects/s_001/mri/transforms/reg.mni152.1mm.dat
----- Mensaje original ----- De: Douglas N Greve <gr...@nmr.mgh.harvard.edu> Fecha: Jueves, 27 de Marzo de 2014, 5:54 pm Asunto: Re: [Freesurfer] MNI CONVERSION PROBLEM A: freesurfer@nmr.mgh.harvard.edu > > The first one should be correct. How are you visualizing it? > What is the > command line? > > > On 03/27/2014 04:26 AM, Gabriel Gonzalez Escamilla wrote: > > I have used both for the output of mni152reg: > > > > mri_vol2vol --mov > > /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -- > targ > > /root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg > > > /root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat > > > --inv --o > > > /root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/mni152.orig.mgz> > > and > > > > mri_vol2vol --targ > > /root/trabajo/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz -- > mov > > /root/trabajo/freesurfer/subjects/s_001/mri/aseg.mgz --reg > > > /root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/transforms/reg.mni152.1mm.dat > > > --o > > > /root/trabajo/freesurfer/subjects/AngelaColesterol_average/mri/orig_in_mni152.mgz> > > I also have tried these two commands with the output matrix of > > bbregister s001_register.dat > > > > > > > > ----- Mensaje original ----- > > De: Douglas Greve <gr...@nmr.mgh.harvard.edu> > > Fecha: Jueves, 27 de Marzo de 2014, 4:11 am > > Asunto: Re: [Freesurfer] MNI CONVERSION PROBLEM > > A: freesurfer@nmr.mgh.harvard.edu > > > > > > > > What is your vol2vol command line? > > > > > > > > > > >On 3/26/14 3:58 PM, Gabriel Gonzalez Escamilla wrote: > >> >Dear FS experts, > >> > > >> > > >> > I've been dealing with the conversion to MNI152 of some > volumetric > >> labels of my subjects extracted with mris_extract_label in FS > v.5.1 > >> but, I've been unable to succeed. > >> > > >> > > >> > I've tried bbregister and mni152reg commands, both of them > give me > >> an example to check at the registrations using tktegister2, > when I > >> use it everything seems to be OK, but when I do apply with > >> mri_vol2vol any of the matrices to the volumetric masks, they > appear > >> to be rotated, I don't know how is it possible or how to fix it. > >> > > >> > > >> > Any help will be really appreciated. > >> > > >> > > >> > Many thanks in advanced, > >> > Gabriel > >> > >> > > >> >_______________________________________________ > Freesurfer > mailing list >Freesurfer@nmr.mgh.harvard.edu > <javascript:main.compose('new', 't=Freesurfer@nmr.mgh.harvard.edu')> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > _______________________________________________ > > > 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. > > > > <font size="3">--------------------------<br />PhD. > student Gabriel > > González-Escamilla<br />Laboratory of Functional > Neuroscience<br > > />Department of Physiology, Anatomy, and Cell Biology<br > />University > > Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - > Seville<br > > />- Spain -<br /><br />Email: ggon...@upo.es<br > > />http://www.upo.es/neuroaging/es/</font> > > > > > > _______________________________________________ > > 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 <font size="3">--------------------------<br />PhD. student Gabriel González-Escamilla<br />Laboratory of Functional Neuroscience<br />Department of Physiology, Anatomy, and Cell Biology<br />University Pablo de Olavide<br />Ctra. de Utrera, Km.1<br />41013 - Seville<br />- Spain -<br /><br />Email: ggon...@upo.es<br />http://www.upo.es/neuroaging/es/</font>
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