Hi FreeSurfer experts, I would need to use the registration tools in freesurfer because the fsl ones ga ve me some problem. Just to try I have run mri_ca_registration and mri_cvs_registration and so I hav e three questions:
1) mri_ca_registration generates a talairach tansform file in .m3z format and I would need to apply it to my high res image. Any hint? 2) Converting RB_all_2008-03-26.gca to nii and opening it to mricron it seems to superimposable to the mni atlas. does it mean that what it comes out from mri_c a_registration coincides to an mni atlas image? 3) Running mri_cvs_registration (on bert data...just to try) I do not know where to find the registered volume file (I have tried few volume .mgz but with no su ccess...). Should i look for a transform file too?
Thanks so much! Martina
mri_vol2vol or mri_convert can apply the .m3z.
RB_all_2008-03-26.gca contains more info than just the means, but we do construct it to be approximately in the MNI space, and part of it can be visualized when you mri_convert it to a volume format (the mean intensity of the most probable label)
Did you read the help for mri_cvs_register? It's pretty extensive (thanks Lilla!)
Bruce
On Thu, 21 Mar 2013, martina.andellini@fastwebnet.it wrote:
Hi FreeSurfer experts, I would need to use the registration tools in freesurfer because the fsl ones ga ve me some problem. Just to try I have run mri_ca_registration and mri_cvs_registration and so I hav e three questions:
- mri_ca_registration generates a talairach tansform file in .m3z format
and I
would need to apply it to my high res image. Any hint? 2) Converting RB_all_2008-03-26.gca to nii and opening it to mricron it
seems to
superimposable to the mni atlas. does it mean that what it comes out from
mri_c
a_registration coincides to an mni atlas image? 3) Running mri_cvs_registration (on bert data...just to try) I do not
know where
to find the registered volume file (I have tried few volume .mgz but with
no su
ccess...). Should i look for a transform file too?
Thanks so much! Martina
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Martina,
What was the command that you ran when executing mri_cvs_register. The default outpur directory is $SUBJECTS_DIR/$subject/cvs. The help alos explains how you can change that directory.
--Lilla
On Thu, 21 Mar 2013, Bruce Fischl wrote:
mri_vol2vol or mri_convert can apply the .m3z.
RB_all_2008-03-26.gca contains more info than just the means, but we do construct it to be approximately in the MNI space, and part of it can be visualized when you mri_convert it to a volume format (the mean intensity of the most probable label)
Did you read the help for mri_cvs_register? It's pretty extensive (thanks Lilla!)
Bruce
On Thu, 21 Mar 2013, martina.andellini@fastwebnet.it wrote:
Hi FreeSurfer experts, I would need to use the registration tools in freesurfer because the fsl ones ga ve me some problem. Just to try I have run mri_ca_registration and mri_cvs_registration and so I hav e three questions:
- mri_ca_registration generates a talairach tansform file in .m3z format
and I
would need to apply it to my high res image. Any hint? 2) Converting RB_all_2008-03-26.gca to nii and opening it to mricron it
seems to
superimposable to the mni atlas. does it mean that what it comes out from
mri_c
a_registration coincides to an mni atlas image? 3) Running mri_cvs_registration (on bert data...just to try) I do not
know where
to find the registered volume file (I have tried few volume .mgz but with
no su
ccess...). Should i look for a transform file too?
Thanks so much! Martina
Freesurfer mailing list 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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Lilla Zollei -
martina.andellini＠fastwebnet.it