Thanks!

The MRI_cc works fine. It's just that I want to use the entire wmparc, and I worry that it may be skewed when the cc is not in there. The cingulate parcellations look a little off. Do you think there's any step in -autorecon2 (before -cortribbon) after the aseg I might try to start reprocessing to fix this?

Best,

Kristine

Hi Kristine,

you can just run mri_cc directly if you want:

mri_cc -o aseg_with_cc.mgz $subject

cheers, Bruce On Tue, 22 Jan 2008 walhovd@nmr.mgh.harvard.edu wrote:

...

Hi

I have a dataset originally processed with the Autumn 2005 FS version (2.2?). I know need wm segs, and in order to get this, I've tried to run

-cortribbon -cortparc -cortparc2 -aparc2aseg -wmparc

But the cc doesn't get labeled in the cortparc, and consequently (?) not in the wmparc either.

I've also tried to rerun all of -autorecon3, but w/o difference.

When rerunning recon-all -all, it gets fixed, but I would like to keep as much as possible as is, since I did lots of edits due to a temporal bias field problem. I've edited the asegs in some instances, and that is not kept by default.

Grateful for tips on how far down in the processing stream I need to go to get correct wmparcs w/cc.

Thanks,

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

Kristine, You should be able to use -ccseg which occurs after the aseg is created in -autorecon2. First, you will need to copy your aseg.mgz to aseg.auto.mgz as this is the file that -ccseg will work on (in the dev version of FS, it uses the aseg.mgz). Allison

On Tue, 22 Jan 2008 k.b.walhovd@psykologi.uio.no wrote:

Thanks!

The MRI_cc works fine. It's just that I want to use the entire wmparc, and I worry that it may be skewed when the cc is not in there. The cingulate parcellations look a little off. Do you think there's any step in -autorecon2 (before -cortribbon) after the aseg I might try to start reprocessing to fix this?

Best,

Kristine

...

Hi Kristine,

you can just run mri_cc directly if you want:

mri_cc -o aseg_with_cc.mgz $subject

cheers, Bruce On Tue, 22 Jan 2008 walhovd@nmr.mgh.harvard.edu wrote:

...

Hi

I have a dataset originally processed with the Autumn 2005 FS version (2.2?). I know need wm segs, and in order to get this, I've tried to run

-cortribbon -cortparc -cortparc2 -aparc2aseg -wmparc

But the cc doesn't get labeled in the cortparc, and consequently (?) not in the wmparc either.

I've also tried to rerun all of -autorecon3, but w/o difference.

When rerunning recon-all -all, it gets fixed, but I would like to keep as much as possible as is, since I did lots of edits due to a temporal bias field problem. I've edited the asegs in some instances, and that is not kept by default.

Grateful for tips on how far down in the processing stream I need to go to get correct wmparcs w/cc.

Thanks,

Kristine _______________________________________________ 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

That should be fine (-ccseg -cortribbon -cortparc -aparc2aseg -wmparc). Allison

On Wed, 23 Jan 2008 k.b.walhovd@psykologi.uio.no wrote:

Thanks, I'll try that. Will I then need to redo all steps fromm -ccseg onwards if I want a correct wmparc at the end, or can I safely skip some? For instance, I could do -ccseg -cortribbon -cortparc -aparc2aseg -wmparc?

Best,

Kristine

...

Kristine, You should be able to use -ccseg which occurs after the aseg is created in -autorecon2. First, you will need to copy your aseg.mgz to aseg.auto.mgz as this is the file that -ccseg will work on (in the dev version of FS, it uses the aseg.mgz). Allison

On Tue, 22 Jan 2008 k.b.walhovd@psykologi.uio.no wrote:

...

Thanks!

The MRI_cc works fine. It's just that I want to use the entire wmparc, and I worry that it may be skewed when the cc is not in there. The cingulate parcellations look a little off. Do you think there's any step in -autorecon2 (before -cortribbon) after the aseg I might try to start reprocessing to fix this?

Best,

Kristine

...

Hi Kristine,

you can just run mri_cc directly if you want:

mri_cc -o aseg_with_cc.mgz $subject

cheers, Bruce On Tue, 22 Jan 2008 walhovd@nmr.mgh.harvard.edu wrote:

...

Hi

I have a dataset originally processed with the Autumn 2005 FS version (2.2?). I know need wm segs, and in order to get this, I've tried to run

-cortribbon -cortparc -cortparc2 -aparc2aseg -wmparc

But the cc doesn't get labeled in the cortparc, and consequently (?) not in the wmparc either.

I've also tried to rerun all of -autorecon3, but w/o difference.

When rerunning recon-all -all, it gets fixed, but I would like to keep as much as possible as is, since I did lots of edits due to a temporal bias field problem. I've edited the asegs in some instances, and that is not kept by default.

Grateful for tips on how far down in the processing stream I need to go to get correct wmparcs w/cc.

Thanks,

Kristine _______________________________________________ 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