Hi Doug,

Thanks a lot, this almost worked! I have one more issue.

The template volume is an axial volume. It was loaded in tkmedit, and the ROI was drawn on its coronal view, and then saved as a label file.

After running mri_label2vol the resulting ANALYZE file displays the ROI incorrectly. What we drew on the coronal view, shows up in the axial, etc.

How can we correct this? (w/ --reg flag?)

Thanks a lot! George P.

On Wed, 2 Mar 2005, Doug Greve wrote:

Hi George,

use mri_label2vol. Run with --help to get docs. You'll need to run it something like:

mri_label2vol --label lh-avg_central_sulcus.label --temp f.img --o lh-avg_central_sulcus.img

--temp is the template volume. The output volume (lh-avg_central_sulcus.img) will have the same geometry as the template.

doug

George Papadimitriou wrote:

...

Hi guys,

I need to convert a label file into analyze, and see if I can import it to the Syngo as an ROI. How can I do this?

I recall reading in an FS-FAST manual about a label2roi program. I don't see it in the standard nmr environment.

I'd really appreciate your input.

George P.

On Wed, 2 Mar 2005, Ruopeng Wang wrote:

...

Hi George,

I have no idea what tkmedit's label file is. I never used tkmedit for real. But I remember some time ago, someone, maybe Judith, converted one to Analyze format, with help from one of tkmedit's developers (maybe Doug).

Ruopeng

On Wed, 2 Mar 2005, George Papadimitriou wrote:

...

Hi Ruopeng,

Are you familiar with tkmedit's label files? They are used to select an ROI. I would like to convert them into ANALYZE and import them into the Syngo. Have you done this before? What are your suggestions?

Thanks, George P.

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

Hi Doug,

The data is in:

/space/thursday/users/greve

The lowb prefixed bfloat volume was the one on which the ROI was drawn on (saved as test.label). If I was to tkmedit this volume, and load the test.label file, everything looks ok.

Then, I converted the volume into ANALYZE (using mri_convert):

mri_convert lowb_000.bfloat lowb.img

lowb.img is the intended --temp input for mri_label2vol.

The problem is that when I load lowb.img in tkmedit, and overlay the test.label file, it does not display properly. Can you please take a look? Thanks!!

Can I come by your desk?

George P.

On Thu, 3 Mar 2005, Doug Greve wrote:

Can you send me command-lines and pointers to your data?

George Papadimitriou wrote:

...

Hi Doug,

Thanks a lot, this almost worked! I have one more issue.

The template volume is an axial volume. It was loaded in tkmedit, and the ROI was drawn on its coronal view, and then saved as a label file.

After running mri_label2vol the resulting ANALYZE file displays the ROI incorrectly. What we drew on the coronal view, shows up in the axial, etc.

How can we correct this? (w/ --reg flag?)

Thanks a lot! George P.

On Wed, 2 Mar 2005, Doug Greve wrote:

...

Hi George,

use mri_label2vol. Run with --help to get docs. You'll need to run it something like:

mri_label2vol --label lh-avg_central_sulcus.label --temp f.img --o lh-avg_central_sulcus.img

--temp is the template volume. The output volume (lh-avg_central_sulcus.img) will have the same geometry as the template.

doug

George Papadimitriou wrote:

...

Hi guys,

I need to convert a label file into analyze, and see if I can import it to the Syngo as an ROI. How can I do this?

I recall reading in an FS-FAST manual about a label2roi program. I don't see it in the standard nmr environment.

I'd really appreciate your input.

George P.

On Wed, 2 Mar 2005, Ruopeng Wang wrote:

...

Hi George,

I have no idea what tkmedit's label file is. I never used tkmedit for real. But I remember some time ago, someone, maybe Judith, converted one to Analyze format, with help from one of tkmedit's developers (maybe Doug).

Ruopeng

On Wed, 2 Mar 2005, George Papadimitriou wrote:

...

Hi Ruopeng,

Are you familiar with tkmedit's label files? They are used to select an ROI. I would like to convert them into ANALYZE and import them into the Syngo. Have you done this before? What are your suggestions?

Thanks, George P.

---

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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422