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I have a few T1 scans that have obvious incorrect registration to mni_average_305. I opened tkregister2 --s subjid --fstal --surfs and I am able to fix the registration, but I wonder how to use the ew registration to recalculate the new ICV. I am interested in doing it with Freesurfer (as I know I could get the matrix and calculate the determinant. I guess I will have to save the transform and rerun some of Freesurfer command to overwrite the old icv value?
Thanks
Gabriel
Just run recon-all -s subject -segstats and the new ICV should appear in the aseg.stats file
On 11/13/2018 12:08 PM, Gamaliz wrote:
External Email - Use Caution
I have a fewT1 scans that have obvious incorrect registration to mni_average_305. I opened tkregister2 --s subjid --fstal --surfs and I am able to fix the registration, but I wonder how to use the ew registration to recalculate the new ICV. I am interested in doing it with Freesurfer (as I know I could get the matrix and calculate the determinant. I guess I will have to save the transform and rerun some of Freesurfer command to overwrite the old icv value?
Thanks
Gabriel
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Once I manually fix the registration how do I save it? I know there is SAVE REG. Will this overwrite the previous file automatically?
On Tue, Nov 13, 2018 at 12:13 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Just run recon-all -s subject -segstats and the new ICV should appear in the aseg.stats file
On 11/13/2018 12:08 PM, Gamaliz wrote:
External Email - Use CautionI have a fewT1 scans that have obvious incorrect registration to mni_average_305. I opened tkregister2 --s subjid --fstal --surfs and I am able to fix the registration, but I wonder how to use the ew registration to recalculate the new ICV. I am interested in doing it with Freesurfer (as I know I could get the matrix and calculate the determinant. I guess I will have to save the transform and rerun some of Freesurfer command to overwrite the old icv value?
Thanks
Gabriel
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
External Email - Use Caution
Great, that worked. I tried it and everything else stayed the same except for the ICV. Thanks
:)
On Tue, Nov 13, 2018 at 12:22 PM Gamaliz gliza002@fiu.edu wrote:
Once I manually fix the registration how do I save it? I know there is SAVE REG. Will this overwrite the previous file automatically?
On Tue, Nov 13, 2018 at 12:13 PM Greve, Douglas N.,Ph.D. < DGREVE@mgh.harvard.edu> wrote:
Just run recon-all -s subject -segstats and the new ICV should appear in the aseg.stats file
On 11/13/2018 12:08 PM, Gamaliz wrote:
External Email - Use CautionI have a fewT1 scans that have obvious incorrect registration to mni_average_305. I opened tkregister2 --s subjid --fstal --surfs and I am able to fix the registration, but I wonder how to use the ew registration to recalculate the new ICV. I am interested in doing it with Freesurfer (as I know I could get the matrix and calculate the determinant. I guess I will have to save the transform and rerun some of Freesurfer command to overwrite the old icv value?
Thanks
Gabriel
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
-- gAbE
Yes, use the SAVE REG button. You should be able to see that it has changed.
On 11/13/2018 12:22 PM, Gamaliz wrote:
External Email - Use Caution
Once I manually fix the registration how do I save it? I know there is SAVE REG. Will this overwrite the previous file automatically?
On Tue, Nov 13, 2018 at 12:13 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> wrote:
Just run recon-all -s subject -segstats and the new ICV should appear in the aseg.stats file On 11/13/2018 12:08 PM, Gamaliz wrote: > > External Email - Use Caution > > > I have a fewT1 scans that have obvious incorrect registration > to mni_average_305. I opened tkregister2 --s subjid --fstal --surfs > and I am able to fix the registration, but I wonder how to use the ew > registration to recalculate the new ICV. I am interested in doing it > with Freesurfer (as I know I could get the matrix and calculate the > determinant. I guess I will have to save the transform and rerun some > of Freesurfer command to overwrite the old icv value? > > > Thanks > > > Gabriel > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer-- gAbE
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Gamaliz -
Greve, Douglas N.,Ph.D.