OK. I ended up using sfa-sess to save time at the command line. Now how do I run pain-sess on abblocked data? It requires that I input a contrast.

1. Is aparc+aseg.mgz supposed to contain the parcellated volume from subcortical and cortical parcellations?

2. We have manually parcellated volumes of the cerebellum. Is there a way we can incorporate this knowledge into autoseg process? Or is there an automatic lobular parcellation system for the cerebellum already? I understand that most T1 images don't have the resolution to do fine surface structure for the cerebellum, but here I'm looking for rough volume parcellation based on the major fissures.

Thanks,

Satra

-- Satrajit Ghosh, PhD

Speech Communication Group Research Laboratory of Electronics, MIT http://spouch.mit.edu/~satra

Satra,

The wiki page for cortical parcellation is found here:

https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation

A wiki page describing the steps in building an atlas for subcortical segmentation (aseg) does not yet exist. If you like I could help you create one and write it :) I've attached a script we use to rebuild an aseg atlas. Its cryptic, and can use some decoding (and an accompanying wiki page), buts it's a start.

I'm not sure I fully understand what you want to do though. Do you want to parcellate the cerebellum based on curvature? I'm not sure this has been attempted (or possible, ie getting cerebellum curvature info). Volumetric segmentation of the cerebellum has been attempted though (but again, no wiki page yet).

Let me know what you want to do.

Nick

On Fri, 2006-05-19 at 18:08 -0400, Bruce Fischl wrote:

Hi Satra,

I guess you could incorporate your cerebellar labels into the aseg. Not sure how accurate it would be, but should be easy to try. Use mri_ca_train to create a new atlas after putting your manual labels in. Nick: is there a wiki page outlining this procedure?

cheers, Bruce

On Fri, 19 May 2006, Satrajit Ghosh wrote:

...

1. Is aparc+aseg.mgz supposed to contain the parcellated volume from

subcortical and cortical parcellations?

2. We have manually parcellated volumes of the cerebellum. Is there a way we

can incorporate this knowledge into autoseg process? Or is there an automatic lobular parcellation system for the cerebellum already? I understand that most T1 images don't have the resolution to do fine surface structure for the cerebellum, but here I'm looking for rough volume parcellation based on the major fissures.

Thanks,

Satra

-- Satrajit Ghosh, PhD

Speech Communication Group Research Laboratory of Electronics, MIT http://spouch.mit.edu/~satra

---

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

I read a while back the tutorial data had been reprocessed with version 3.0, but not uploaded yet. Is the new data uploaded now? If so, is this the correct dataset for the morphometry and reconstruction tutorial? ftp://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_data-tutorial_subjs.tar.gz

(The datestamps on the ftp says January-something.)

Thanks Inge Amlien

That's great Nick, thanks.

/Inge

-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: 23. mai 2006 00:44 To: Inge Kasbohm Amlien Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] Tutorial data

Inge,

Funny you should ask. We are busily updating this data right now in preparation for an upcoming Freesurfer course. The data should be posted for download by the end of the week (along with an updated tutorial wiki).

We'll post to this mailing list when it is ready.

However, the existing dataset and wiki tutorial is entirely compatible with version 3.0. The updates just account for the fact that freesurfer v3.0 fixes more defects than prior freesurfer versions, so some defects will no longer exist in the updated dataset.

Nick

On Tue, 2006-05-23 at 00:24 +0200, Inge Kasbohm Amlien wrote:

I read a while back the tutorial data had been reprocessed with version

3.0,

but not uploaded yet. Is the new data uploaded now? If so, is this the correct dataset for the morphometry and reconstruction tutorial?

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/buckner_data-tutorial_subjs.tar.gz

(The datestamps on the ftp says January-something.)

Thanks Inge Amlien

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer