Hello, I would like to register a 2D EPI oblique axial slice to a 3D MPRAGE and am hoping that Freesurfer will help me do this. I have not had any luck with other fMRI software packages. Caveat: Each subject's EPI axial slice was taken parallel to his/her specific hippocampal longitudinal axis and the angle is unknown. Therefore, I have a low-res 2D axial slice at an unknown angle and a high-res 3D MPRAGE.
Is Freesurfer capable of finding and applying the appropriate transformation? Specific suggestions would be greatly appreciated.
Best, Susie
Hi Susie, I have a tool that works very well on this type of thing, but I am not quite ready to release it (a few more weeks). It will be greatly facilitated if you acquired a whole-brain image during your scan (this can include the MPRAGE itself). If not, then you'll have to do some hand registration to get it close (if you collect more data of this type, make sure to get a whole-brain scan -- virtually anything will do, including a single time point from an epi).
doug
Susie Heo wrote:
Hello, I would like to register a 2D EPI oblique axial slice to a 3D MPRAGE and am hoping that Freesurfer will help me do this. I have not had any luck with other fMRI software packages. Caveat: Each subject's EPI axial slice was taken parallel to his/her specific hippocampal longitudinal axis and the angle is unknown. Therefore, I have a low-res 2D axial slice at an unknown angle and a high-res 3D MPRAGE.
Is Freesurfer capable of finding and applying the appropriate transformation? Specific suggestions would be greatly appreciated.
Best, Susie
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi list! I am experiencing a problem when reprocessing 70-something previously edited (FS 4.05) subjects on FS version 4.10. It seems fill fails, but no errors are returned. I cannot find anything in the logs either. The problem is not present when starting over fresh and processing from dicoms, at least for the one subject I tried.
Any tips on what to try appreciated!
See attached images, it is the same subject, the same slice, version 4.10 on the left, 4.05 on the right.
FREESURFER_HOME: /psyklab/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-53.1.6.el5.centos.plus x86_64 recon-all -all -s $id
Have a nice day Inge Amlien Center for the Study of Human Cognition University of Oslo Norway
Hi Inge,
what does the aseg look like? Are the ventricles and caudate properly labeled in both versions?
Bruce
On Tue, 2 Dec 2008, Inge K. Amlien wrote:
Hi list! I am experiencing a problem when reprocessing 70-something previously edited (FS 4.05) subjects on FS version 4.10. It seems fill fails, but no errors are returned. I cannot find anything in the logs either. The problem is not present when starting over fresh and processing from dicoms, at least for the one subject I tried.
Any tips on what to try appreciated!
See attached images, it is the same subject, the same slice, version 4.10 on the left, 4.05 on the right.
FREESURFER_HOME: /psyklab/local/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.1.0 RedHat release: CentOS release 5 (Final) Kernel info: Linux 2.6.18-53.1.6.el5.centos.plus x86_64 recon-all -all -s $id
Have a nice day Inge Amlien Center for the Study of Human Cognition University of Oslo Norway
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Doug Greve -
Inge K. Amlien -
Susie Heo