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:greve@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:greve@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-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@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
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