Hi Prasanna,

yes, simply looking at the label in aseg.mgz is fine. I don't think pretess is part of recon-all and it may happen, that these labels are not very smooth. Pretess helps a little (but this is mainly important for people who generate a surface mesh from the label). For you it is probably not necessary.

best Martin

p.s please always reply to the list so that others can answer.

On Dec 8, 2012, at 3:18 PM, Prasanna M prasanna@sci.utah.edu wrote:

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, Prasanna

On 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.

--------------------------------- Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT

A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129

Phone: +1-617-724-5652 Email: mreuter@nmr.mgh.harvard.edu reuter@mit.edu Web : http://reuter.mit.edu