Hi Martin,For each subject and each time-point, I did the cross-sectional processing. Then I ran the recon-all base to create templates for each subject. Then I ran the recon-all long to do the longitudinal processing. I ran each of these commands with the -all option. Isn't mri_pretess part of the recon-all stage already? Do I need to use it again to clean up voxels?So for each subject and each time-point, I have all the segmentations with labels for each subcortical structures, say 17 for the left hippocampus, and 53 for the right hippocampus. So would I need only to threshold each of these aseg.mgz files at these values to get an accurate segmentation of structures? Or would I need to do something more? I'm new to image processing, so I apologize if these questions seem too trivial.Thanks,PrasannaOn Fri, Dec 7, 2012 at 11:45 AM, Prasanna M <prasanna@sci.utah.edu> wrote:
Thanks martin. My mistake. nothing to do with longitudinal processing. Wanted to be able to segment out each structure. I'll look up mri_pretess.Thanks.On Fri, Dec 7, 2012 at 11:27 AM, Martin Reuter <mreuter@nmr.mgh.harvard.edu> wrote:Hi Prasanna,
not sure what you are asking and what this has to do with longitudinal.
But generally: subcortical segmentations are stored in the aseg.mgz file
(this is true also for the longituinal stream, do not look at the
aseg.fused.mgz , it is an intermediate step). Final results are in
aseg.mgz.
Aparc is for the parcellations of the cortex.
Freesurfer has tools to create e.g. a hippocampus mask from the aseg.
mri_pretess can probably do it and cleans up the mask a little.
Best, Martin
> _______________________________________________
On Fri, 2012-12-07 at 11:04 -0700, Prasanna M wrote:
> Hi,
>
>
> Do I work with aseg.fused.mgz or do I work with aparc files to get the
> most accurate segmentation of brain structures?
>
>
>
> I tried using freeview to look at segmentations. Is there a way to
> isolate mgz files of very specific structures. I mean, is there an
> inbuilt tool which can do that for me, or would I have to go image by
> image, and threshold to get, say the hippocampus?
>
>
> Thanks,
> Prasanna
>
>
>
>
>
> --
> --
> Let there be peace on earth...
> And let it begin with me.
>
>
>
>
>
>
>
> 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.
----Let there be peace on earth...
And let it begin with me.
----Let there be peace on earth...
And let it begin with me.