btw, you can have mri_vol2vol convert directly to analyze by using a .img extension. But why use analyze?

joel bruss wrote:

Nick-

Doug wrote:

...

Try this:

...

mri_vol2vol --mov aseg.mgz --targ rawavg.mgz --o aseg-in-native.mgz --regheader --interp nearest

...

doug

Sure enough, this worked. What I mean by "norm" is the file /mri/norm.mgz which gets created in the CA Normalize section of recon-all. Mike was kind enough to point out that this is the same as orig.mgz but, this was not what I was going after. What I meant by "native" was the T1 volume I input into freesurfer (before conversion from Analzye to mgz via mri_convert). After running Doug's command, and converting back to Analyze format, I now have a working copy of "aseg" (sub-cortical) that can be overlaid onto my, original, native space T1 MRI.

Thanks everyone for your help.

-Joel

On Nov 13, 2007 12:43 PM, Nick Schmansky nicks@nmr.mgh.harvard.edu wrote:

...

Joel,

All freesurfer volume files, including aseg.mgz, are in native MRI space. The various talairach transforms are used to align to the atlases used in freesurfer. I'm not sure what you mean by 'norm' space. The --apply_transform flag of mri_convert can be used to convert a volume to talairach space (see mri_convert --help for details).

Nick

On Tue, 2007-11-13 at 12:01 -0600, joel bruss wrote:

...

Hello-

I'm running FreeSurfer v4.01on SUSE Linux

I'm interested in viewing the sub-cortical parcels, /mri/aseg.mgz, but in the native MRI space. I see that the output of "CA Label" produces a file that is fit to the "CA Normalize" step but I can't figure out the transform that was used. Specifically, for CA Normalize, if I look under /mri/transforms, and sort by time, I have both the talairach.lta and talairach.m3z files, but neither will get me from native to norm space (or vice-versa). Is there a transform file that I'm missing or is this a process of intermediate steps to get from native to norm space? Please help!

Thanks, Joel

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This is the last question that I have...sorry to keep bothering you all. Is there a page on the FS wiki or is there a man page that details the value of each sub-cortical parcel? I see that each masked are has a value (1, 2, 3, etc.) but before I make assumptions about which values correspond with which region, I though I'd ask for help.

-Joel

On Nov 13, 2007 1:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Joel,

both the .m3z (nonlinear) and the .lta (linear) are transforms from the subject to the atlas coordinate system, but all the labeling is done in the subject space, so you should be set.

cheers, Bruce On Tue, 13 Nov 2007, joel bruss wrote:

...

Hello-

I'm running FreeSurfer v4.01on SUSE Linux

I'm interested in viewing the sub-cortical parcels, /mri/aseg.mgz, but in the native MRI space. I see that the output of "CA Label" produces a file that is fit to the "CA Normalize" step but I can't figure out the transform that was used. Specifically, for CA Normalize, if I look under /mri/transforms, and sort by time, I have both the talairach.lta and talairach.m3z files, but neither will get me from native to norm space (or vice-versa). Is there a transform file that I'm missing or is this a process of intermediate steps to get from native to norm space? Please help!

Thanks, Joel

...

---

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

and the papers describing the subcortical segmentation scheme are found at the bottom of the main wiki page:

http://surfer.nmr.mgh.harvard.edu/fswiki

in the section 'subcortical segmentation'.

On Tue, 2007-11-13 at 15:17 -0500, Doug Greve wrote:

Look in $FREESURFER_HOME/FreeSurferColorLUT.txt

doug

joel bruss wrote:

...

This is the last question that I have...sorry to keep bothering you all. Is there a page on the FS wiki or is there a man page that details the value of each sub-cortical parcel? I see that each masked are has a value (1, 2, 3, etc.) but before I make assumptions about which values correspond with which region, I though I'd ask for help.

-Joel

On Nov 13, 2007 1:09 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

...

Hi Joel,

both the .m3z (nonlinear) and the .lta (linear) are transforms from the subject to the atlas coordinate system, but all the labeling is done in the subject space, so you should be set.

cheers, Bruce On Tue, 13 Nov 2007, joel bruss wrote:

...

Hello-

I'm running FreeSurfer v4.01on SUSE Linux

I'm interested in viewing the sub-cortical parcels, /mri/aseg.mgz, but in the native MRI space. I see that the output of "CA Label" produces a file that is fit to the "CA Normalize" step but I can't figure out the transform that was used. Specifically, for CA Normalize, if I look under /mri/transforms, and sort by time, I have both the talairach.lta and talairach.m3z files, but neither will get me from native to norm space (or vice-versa). Is there a transform file that I'm missing or is this a process of intermediate steps to get from native to norm space? Please help!

Thanks, Joel

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In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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