Re: [Freesurfer] Asymmetries of cortical thickness
Hi Sophie, you can run the following command: cd $SUBJECTS_DIR/yoursubject mris_apply_reg --src xhemi/surf/lh.thickness --streg xhemi/surf/lh.fsaverage_sym.sphere.reg surf/lh.fsaverage_sym.sphere.reg --tval surf/lh.rh.thickness.mgh lh.rh.thickness.mgh will now have the rh thicknesses on the rh surface mris_apply_reg is only available in 5.2. If you don't have 5.2, I can get you a version of this program if you tell me your OS. Also note that you need to go through the xhemi-reg procedure first. doug On 03/18/2013 10:40 AM, Sophie Maingault wrote: > Yes if it is possible I would like to know how to do it ? > > Thanks ! > > Sophie > > -Message d'origine- > De : Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Envoyé : lundi 18 mars 2013 14:39 > À : Sophie Maingault; Freesurfer@nmr.mgh.harvard.edu > Objet : Re: [Freesurfer] Asymmetries of cortical thickness > > It is possible, it is just not a good idea because if you map rh to lh > and then compare to lh, the rh will have been interpolated to get it > into the lh. Even if there are no differences between the two, you will > see differences because of the interpolation. Mapping both to > fsaverage_sym means that both will be interpolated. If this > interpolation does not bother you, then I can show you how to get it > from rh to lh. > doug > > > > > On 03/18/2013 09:24 AM, Sophie Maingault wrote: >> So i didn't understand what you mean by "just specify one subject when > your >> mris_preproc" ? Because, in fact I don't want to use the registration on >> fsaverage_sym. I would like just to create a file lh.thickness less >> rh.thickness vertex per vertex, maybe it is not possible ? >> >> -Message d'origine- >> De : Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] >> Envoyé : lundi 18 mars 2013 14:15 >> À : Sophie Maingault; Freesurfer@nmr.mgh.harvard.edu >> Objet : Re: [Freesurfer] Asymmetries of cortical thickness >> >> No, it is not, the target needs to be fsaverage_sym >> doug >> >> >> On 03/18/2013 09:13 AM, Sophie Maingault wrote: >>> So I do : mris_preproc --target fsaverage --xhemi --hemi lh --paired-diff >>> --meas thickness --out lh.lh-rh.thickness.sm00.mgh --s t0001 --s t0003 > --s >>> t0009 --s t0027 --s t0031 --s t0033 --s t0126 --s t0148 --s t0171 --s >> t0174 >>> --s t0199 --s t0203 --s t0212 --s t0215 --s t0242 --s t0245 --s t0253 --s >>> t0254 --s t0256 --s t0268 >>> >>> You think it's ok ? >>> >>> Sophie >>> >>> -Message d'origine- >>> De : freesurfer-boun...@nmr.mgh.harvard.edu >>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] De la part de Douglas N >>> Greve >>> Envoyé : lundi 18 mars 2013 13:49 >>> À : freesurfer@nmr.mgh.harvard.edu >>> Objet : Re: [Freesurfer] Asymmetries of cortical thickness >>> >>> you will have to use the same stream, just specify one subject when your >>> mris_preproc >>> doug >>> >>> >>> On 03/18/2013 08:06 AM, Sophie Maingault wrote: >>>> Hello, >>>> >>>> Iobtained a map of cortical thickness asymmetries after the >>>> registration on the symmetric atlas. But I would to obtain the same >>>> map with raw data I mean just by subtract lh.thickness and >>>> rh.thickness. How can I modify the part #Create a stack of subjects in >>>> wiki page ? I have to register to fsaverage (and not fsaverage_sym) >>>> and then do the same thing ? >>>> >>>> Thanks you for your help. >>>> >>>> Sophie >>>> >>>> >>>> >>>> ___ >>>> 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: 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 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.
Re: [Freesurfer] Asymmetries of cortical thickness
It is possible, it is just not a good idea because if you map rh to lh and then compare to lh, the rh will have been interpolated to get it into the lh. Even if there are no differences between the two, you will see differences because of the interpolation. Mapping both to fsaverage_sym means that both will be interpolated. If this interpolation does not bother you, then I can show you how to get it from rh to lh. doug On 03/18/2013 09:24 AM, Sophie Maingault wrote: > So i didn't understand what you mean by "just specify one subject when your > mris_preproc" ? Because, in fact I don't want to use the registration on > fsaverage_sym. I would like just to create a file lh.thickness less > rh.thickness vertex per vertex, maybe it is not possible ? > > -Message d'origine- > De : Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] > Envoyé : lundi 18 mars 2013 14:15 > À : Sophie Maingault; Freesurfer@nmr.mgh.harvard.edu > Objet : Re: [Freesurfer] Asymmetries of cortical thickness > > No, it is not, the target needs to be fsaverage_sym > doug > > > On 03/18/2013 09:13 AM, Sophie Maingault wrote: >> So I do : mris_preproc --target fsaverage --xhemi --hemi lh --paired-diff >> --meas thickness --out lh.lh-rh.thickness.sm00.mgh --s t0001 --s t0003 --s >> t0009 --s t0027 --s t0031 --s t0033 --s t0126 --s t0148 --s t0171 --s > t0174 >> --s t0199 --s t0203 --s t0212 --s t0215 --s t0242 --s t0245 --s t0253 --s >> t0254 --s t0256 --s t0268 >> >> You think it's ok ? >> >> Sophie >> >> -Message d'origine- >> De : freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] De la part de Douglas N >> Greve >> Envoyé : lundi 18 mars 2013 13:49 >> À : freesurfer@nmr.mgh.harvard.edu >> Objet : Re: [Freesurfer] Asymmetries of cortical thickness >> >> you will have to use the same stream, just specify one subject when your >> mris_preproc >> doug >> >> >> On 03/18/2013 08:06 AM, Sophie Maingault wrote: >>> Hello, >>> >>> Iobtained a map of cortical thickness asymmetries after the >>> registration on the symmetric atlas. But I would to obtain the same >>> map with raw data I mean just by subtract lh.thickness and >>> rh.thickness. How can I modify the part #Create a stack of subjects in >>> wiki page ? I have to register to fsaverage (and not fsaverage_sym) >>> and then do the same thing ? >>> >>> Thanks you for your help. >>> >>> Sophie >>> >>> >>> >>> ___ >>> 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: 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 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.
Re: [Freesurfer] Asymmetries of cortical thickness
No, it is not, the target needs to be fsaverage_sym doug On 03/18/2013 09:13 AM, Sophie Maingault wrote: > So I do : mris_preproc --target fsaverage --xhemi --hemi lh --paired-diff > --meas thickness --out lh.lh-rh.thickness.sm00.mgh --s t0001 --s t0003 --s > t0009 --s t0027 --s t0031 --s t0033 --s t0126 --s t0148 --s t0171 --s t0174 > --s t0199 --s t0203 --s t0212 --s t0215 --s t0242 --s t0245 --s t0253 --s > t0254 --s t0256 --s t0268 > > You think it's ok ? > > Sophie > > -Message d'origine- > De : freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] De la part de Douglas N > Greve > Envoyé : lundi 18 mars 2013 13:49 > À : freesurfer@nmr.mgh.harvard.edu > Objet : Re: [Freesurfer] Asymmetries of cortical thickness > > you will have to use the same stream, just specify one subject when your > mris_preproc > doug > > > On 03/18/2013 08:06 AM, Sophie Maingault wrote: >> Hello, >> >> Iobtained a map of cortical thickness asymmetries after the >> registration on the symmetric atlas. But I would to obtain the same >> map with raw data I mean just by subtract lh.thickness and >> rh.thickness. How can I modify the part #Create a stack of subjects in >> wiki page ? I have to register to fsaverage (and not fsaverage_sym) >> and then do the same thing ? >> >> Thanks you for your help. >> >> Sophie >> >> >> >> ___ >> 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: 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 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.
Re: [Freesurfer] Asymmetries of cortical thickness
you will have to use the same stream, just specify one subject when your mris_preproc doug On 03/18/2013 08:06 AM, Sophie Maingault wrote: > > Hello, > > Iobtained a map of cortical thickness asymmetries after the > registration on the symmetric atlas. But I would to obtain the same > map with raw data I mean just by subtract lh.thickness and > rh.thickness. How can I modify the part #Create a stack of subjects in > wiki page ? I have to register to fsaverage (and not fsaverage_sym) > and then do the same thing ? > > Thanks you for your help. > > Sophie > > > > ___ > 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: 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 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.
[Freesurfer] Asymmetries of cortical thickness
Hello, I obtained a map of cortical thickness asymmetries after the registration on the symmetric atlas. But I would to obtain the same map with raw data I mean just by subtract lh.thickness and rh.thickness. How can I modify the part #Create a stack of subjects in wiki page ? I have to register to fsaverage (and not fsaverage_sym) and then do the same thing ? Thanks you for your help. Sophie ___ 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.
