spatial scale bar question

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Nasiriavanaki, Zahra

10 May 2019 10 May '19

3:13 p.m.

Dear Freesurfers

I am trying to add a spatial scale bar to my cortical maps in tksurfer. However, as it's mentioned in Freesurfer forum before, the scale bar in tksurfer shrinks when you zoom in the brain.

I couldn't find a scale bar option in Freeview neither.

I appreciate if you could let me know how to get a scale bar.

Thanks

Mona

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Greve, Douglas N.,Ph.D.

10 May 10 May

3:27 p.m.

In freeview, it is just an icon above the image window. Click on it and it should give you a scale bar

On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:

Dear Freesurfers

I am trying to add a spatial scale bar to my cortical maps in tksurfer. However, as it's mentioned in Freesurfer forum before, the scale bar in tksurfer shrinks when you zoom in the brain.

I couldn't find a scale bar option in Freeview neither.

I appreciate if you could let me know how to get a scale bar.

Thanks

Mona

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

Nasiriavanaki, Zahra

3:40 p.m.

Thanks for your reply.

I have overlaid the significance map on an inflated brain, and I don't see the scale bar icon anywhere.

tksurferfv fsaverage lh inflated -ov sig.nii.gz

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Friday, May 10, 2019 3:27:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spatial scale bar question

In freeview, it is just an icon above the image window. Click on it and it should give you a scale bar

On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:

Dear Freesurfers

I am trying to add a spatial scale bar to my cortical maps in tksurfer. However, as it's mentioned in Freesurfer forum before, the scale bar in tksurfer shrinks when you zoom in the brain.

I couldn't find a scale bar option in Freeview neither.

I appreciate if you could let me know how to get a scale bar.

Thanks

Mona

Greve, Douglas N.,Ph.D.

6:13 p.m.

here is a pick of it https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif

On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:

Thanks for your reply.

I have overlaid the significance map on an inflated brain, and I don't see the scale bar icon anywhere.

tksurferfv fsaverage lh inflated -ov sig.nii.gz

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu Sent: Friday, May 10, 2019 3:27:15 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spatial scale bar question

In freeview, it is just an icon above the image window. Click on it and it should give you a scale bar

On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:

Dear Freesurfers

I am trying to add a spatial scale bar to my cortical maps in tksurfer. However, as it's mentioned in Freesurfer forum before, the scale bar in tksurfer shrinks when you zoom in the brain.

I couldn't find a scale bar option in Freeview neither.

I appreciate if you could let me know how to get a scale bar.

Thanks

Mona

Bruce Fischl

6:15 p.m.

I don't think it currently works in 3D mode as it is not trivial due to perspective transforms. Ruopeng is trying some things On Fri, 10 May 2019, Greve, Douglas N.,Ph.D. wrote:

...

here is a pick of it https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif

On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
  Thanks for your reply.

  I have overlaid the significance map on an inflated brain, and I don't see the scale
  bar icon anywhere.

  tksurferfv fsaverage lh inflated -ov sig.nii.gz
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Friday, May 10, 2019 3:27:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spatial scale bar question In freeview, it is just an icon above the image window. Click on it and it should give you a scale bar

On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:
  Dear Freesurfers 

  Hi


  I am trying to add a spatial scale bar to my cortical maps in tksurfer. However,
  as it's mentioned in Freesurfer forum before, the scale bar in tksurfer shrinks
  when you zoom in the brain.

  I couldn't find a scale bar option in Freeview neither.

  I appreciate if you could let me know how to get a scale bar.


  Thanks

  Mona
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

Nasiriavanaki, Zahra

13 May 13 May

9:49 a.m.

Yes Bruce.

It doesn't work.

I appreciate if you could let me know when you had any updates on it.

Thanks

Mona

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Friday, May 10, 2019 6:15:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] spatial scale bar question

I don't think it currently works in 3D mode as it is not trivial due to perspective transforms. Ruopeng is trying some things On Fri, 10 May 2019, Greve, Douglas N.,Ph.D. wrote:

...

here is a pick of it https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif

[https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif]

...

On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
  Thanks for your reply.

  I have overlaid the significance map on an inflated brain, and I don't see the scale
  bar icon anywhere.

  tksurferfv fsaverage lh inflated -ov sig.nii.gz
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Friday, May 10, 2019 3:27:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spatial scale bar question In freeview, it is just an icon above the image window. Click on it and it should give you a scale bar

On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:
  Dear Freesurfers

  Hi


  I am trying to add a spatial scale bar to my cortical maps in tksurfer. However,
  as it's mentioned in Freesurfer forum before, the scale bar in tksurfer shrinks
  when you zoom in the brain.

  I couldn't find a scale bar option in Freeview neither.

  I appreciate if you could let me know how to get a scale bar.


  Thanks

  Mona
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

Bruce Fischl

9:56 a.m.

Hi Mona

sure. As I said it is a bit more complicated than it seems. Ruopeng will post a note when something usable is in the dev version

Bruce

On Mon, 13 May 2019, Nasiriavanaki, Zahra wrote:

...

Yes Bruce.

It doesn't work.

I appreciate if you could let me know when you had any updates on it.

Thanks

Mona

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Friday, May 10, 2019 6:15:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] spatial scale bar question I don't think it currently works in 3D mode as it is not trivial due to perspective transforms. Ruopeng is trying some things On Fri, 10 May 2019, Greve, Douglas N.,Ph.D. wrote:

...
here is a pick of it https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif

[fv.colorbar.gif]

...
On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:

Thanks for your reply.

I have overlaid the significance map on an inflated brain, and I don't see the scale bar icon anywhere.

tksurferfv fsaverage lh inflated -ov sig.nii.gz

_

...
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Friday, May 10, 2019 3:27:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spatial scale bar question In freeview, it is just an icon above the image window. Click on it and it should give you a scale bar

On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:

Dear Freesurfers

Hi

I am trying to add a spatial scale bar to my cortical maps in tksurfer. However, as it's mentioned in Freesurfer forum before, the scale bar in tksurfer shrinks when you zoom in the brain.

I couldn't find a scale bar option in Freeview neither.

I appreciate if you could let me know how to get a scale bar.

Thanks

Mona

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

Nasiriavanaki, Zahra

10:15 a.m.

Great! Thanks

...

On May 13, 2019, at 9:56 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:

Hi Mona

sure. As I said it is a bit more complicated than it seems. Ruopeng will post a note when something usable is in the dev version

Bruce

On Mon, 13 May 2019, Nasiriavanaki, Zahra wrote:

...
Yes Bruce. It doesn't work. I appreciate if you could let me know when you had any updates on it. Thanks Mona ___________________________________________________________________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Friday, May 10, 2019 6:15:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] spatial scale bar question I don't think it currently works in 3D mode as it is not trivial due to perspective transforms. Ruopeng is trying some things On Fri, 10 May 2019, Greve, Douglas N.,Ph.D. wrote:

...
here is a pick of it https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif

[fv.colorbar.gif]

...
On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
  Thanks for your reply.

  I have overlaid the significance map on an inflated brain, and I don't see the scale
  bar icon anywhere.

  tksurferfv fsaverage lh inflated -ov sig.nii.gz
_

...
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Friday, May 10, 2019 3:27:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spatial scale bar question In freeview, it is just an icon above the image window. Click on it and it should give you a scale bar

On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:
  Dear Freesurfers 

  Hi


  I am trying to add a spatial scale bar to my cortical maps in tksurfer. However,
  as it's mentioned in Freesurfer forum before, the scale bar in tksurfer shrinks
  when you zoom in the brain.

  I couldn't find a scale bar option in Freeview neither.

  I appreciate if you could let me know how to get a scale bar.


  Thanks

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

Nasiriavanaki, Zahra

15 Aug 15 Aug

4:30 p.m.

Hi Freesurfer experts

I wanted to follow up on my question about "spatial scale bar" for significancy maps in FS.

I appreciate if you let me know about the updates on that.

Thanks

Mona

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Monday, May 13, 2019 9:56:41 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spatial scale bar question

Hi Mona

sure. As I said it is a bit more complicated than it seems. Ruopeng will post a note when something usable is in the dev version

Bruce

On Mon, 13 May 2019, Nasiriavanaki, Zahra wrote:

...

Yes Bruce.

It doesn't work.

I appreciate if you could let me know when you had any updates on it.

Thanks

Mona

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Friday, May 10, 2019 6:15:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] spatial scale bar question I don't think it currently works in 3D mode as it is not trivial due to perspective transforms. Ruopeng is trying some things On Fri, 10 May 2019, Greve, Douglas N.,Ph.D. wrote:

...
here is a pick of it https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif

[fv.colorbar.gif]

...
On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
  Thanks for your reply.

  I have overlaid the significance map on an inflated brain, and I don't see the scale
  bar icon anywhere.

  tksurferfv fsaverage lh inflated -ov sig.nii.gz
_

...
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Friday, May 10, 2019 3:27:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spatial scale bar question In freeview, it is just an icon above the image window. Click on it and it should give you a scale bar

On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:
  Dear Freesurfers

  Hi


  I am trying to add a spatial scale bar to my cortical maps in tksurfer. However,
  as it's mentioned in Freesurfer forum before, the scale bar in tksurfer shrinks
  when you zoom in the brain.

  I couldn't find a scale bar option in Freeview neither.

  I appreciate if you could let me know how to get a scale bar.


  Thanks

  Mona
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

Ruopeng Wang

16 Aug 16 Aug

8:46 a.m.

Hi Mona,

If you are running the latest dev build, you can right click in the 3D view and choose “Show 3D scale”. The scale bars can only be placed at the boundary of the FOV.

Best, Ruopeng

...

On Aug 15, 2019, at 4:30 PM, Nasiriavanaki, Zahra ZNASIRIAVANAKI@mgh.harvard.edu wrote:

Hi Freesurfer experts

I wanted to follow up on my question about "spatial scale bar" for significancy maps in FS. I appreciate if you let me know about the updates on that.

Thanks Mona

Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Monday, May 13, 2019 9:56:41 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spatial scale bar question

Hi Mona

sure. As I said it is a bit more complicated than it seems. Ruopeng will post a note when something usable is in the dev version

Bruce

On Mon, 13 May 2019, Nasiriavanaki, Zahra wrote:

...
Yes Bruce.

It doesn't work.

I appreciate if you could let me know when you had any updates on it.

Thanks

Mona

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Friday, May 10, 2019 6:15:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] spatial scale bar question I don't think it currently works in 3D mode as it is not trivial due to perspective transforms. Ruopeng is trying some things On Fri, 10 May 2019, Greve, Douglas N.,Ph.D. wrote:

...
here is a pick of it https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif

[fv.colorbar.gif]

...
On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
  Thanks for your reply.

  I have overlaid the significance map on an inflated brain, and I don't see the scale
  bar icon anywhere.

  tksurferfv fsaverage lh inflated -ov sig.nii.gz
_

...
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. DGREVE@mgh.harvard.edu Sent: Friday, May 10, 2019 3:27:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spatial scale bar question In freeview, it is just an icon above the image window. Click on it and it should give you a scale bar

On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:
  Dear Freesurfers 

  Hi


  I am trying to add a spatial scale bar to my cortical maps in tksurfer. However,
  as it's mentioned in Freesurfer forum before, the scale bar in tksurfer shrinks
  when you zoom in the brain.

  I couldn't find a scale bar option in Freeview neither.

  I appreciate if you could let me know how to get a scale bar.


  Thanks

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

Nasiriavanaki, Zahra

10:25 a.m.

Hi Ruopeng

Thanks for your reply.

I have a question though. When I zoom in the 3D image, the scale bar numbers don't change. Shouldn't they change when I zoom in?

Thanks

Mona

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ruopeng Wang rpwang@nmr.mgh.harvard.edu Sent: Friday, August 16, 2019 8:46:57 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spatial scale bar question

Hi Mona,

If you are running the latest dev build, you can right click in the 3D view and choose “Show 3D scale”. The scale bars can only be placed at the boundary of the FOV.

Best, Ruopeng

On Aug 15, 2019, at 4:30 PM, Nasiriavanaki, Zahra <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> wrote:

Hi Freesurfer experts

I wanted to follow up on my question about "spatial scale bar" for significancy maps in FS. I appreciate if you let me know about the updates on that.

Thanks Mona

Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> Sent: Monday, May 13, 2019 9:56:41 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] spatial scale bar question

Hi Mona

sure. As I said it is a bit more complicated than it seems. Ruopeng will post a note when something usable is in the dev version

Bruce

On Mon, 13 May 2019, Nasiriavanaki, Zahra wrote:

...

Yes Bruce.

It doesn't work.

I appreciate if you could let me know when you had any updates on it.

Thanks

Mona

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> Sent: Friday, May 10, 2019 6:15:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] spatial scale bar question I don't think it currently works in 3D mode as it is not trivial due to perspective transforms. Ruopeng is trying some things On Fri, 10 May 2019, Greve, Douglas N.,Ph.D. wrote:

...
here is a pick of it https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif

[fv.colorbar.gif]

...
On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
  Thanks for your reply.

  I have overlaid the significance map on an inflated brain, and I don't see the scale
  bar icon anywhere.

  tksurferfv fsaverage lh inflated -ov sig.nii.gz
_

...
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> Sent: Friday, May 10, 2019 3:27:15 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spatial scale bar question In freeview, it is just an icon above the image window. Click on it and it should give you a scale bar

On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:
  Dear Freesurfers

  Hi


  I am trying to add a spatial scale bar to my cortical maps in tksurfer. However,
  as it's mentioned in Freesurfer forum before, the scale bar in tksurfer shrinks
  when you zoom in the brain.

  I couldn't find a scale bar option in Freeview neither.

  I appreciate if you could let me know how to get a scale bar.


  Thanks

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

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

Ruopeng Wang

10:42 a.m.

The 3D scale is also a 3d object in the view. When you zoom the view, the scale will also zoom. But the number should not change.

...

On Aug 16, 2019, at 10:25 AM, Nasiriavanaki, Zahra ZNASIRIAVANAKI@mgh.harvard.edu wrote:

Hi Ruopeng

Thanks for your reply. I have a question though. When I zoom in the 3D image, the scale bar numbers don't change. Shouldn't they change when I zoom in?

Thanks Mona

Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ruopeng Wang rpwang@nmr.mgh.harvard.edu Sent: Friday, August 16, 2019 8:46:57 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spatial scale bar question

Hi Mona,

If you are running the latest dev build, you can right click in the 3D view and choose “Show 3D scale”. The scale bars can only be placed at the boundary of the FOV.

Best, Ruopeng

...
On Aug 15, 2019, at 4:30 PM, Nasiriavanaki, Zahra <ZNASIRIAVANAKI@mgh.harvard.edu mailto:ZNASIRIAVANAKI@mgh.harvard.edu> wrote:

Hi Freesurfer experts

I wanted to follow up on my question about "spatial scale bar" for significancy maps in FS. I appreciate if you let me know about the updates on that.

Thanks Mona

Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> Sent: Monday, May 13, 2019 9:56:41 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] spatial scale bar question

Hi Mona

sure. As I said it is a bit more complicated than it seems. Ruopeng will post a note when something usable is in the dev version

Bruce

On Mon, 13 May 2019, Nasiriavanaki, Zahra wrote:

...
Yes Bruce.

It doesn't work.

I appreciate if you could let me know when you had any updates on it.

Thanks

Mona

From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> Sent: Friday, May 10, 2019 6:15:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] spatial scale bar question I don't think it currently works in 3D mode as it is not trivial due to perspective transforms. Ruopeng is trying some things On Fri, 10 May 2019, Greve, Douglas N.,Ph.D. wrote:

...
here is a pick of it https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif

[fv.colorbar.gif]

...
On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
  Thanks for your reply.

  I have overlaid the significance map on an inflated brain, and I don't see the scale
  bar icon anywhere.

  tksurferfv fsaverage lh inflated -ov sig.nii.gz
_

...
From: freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu mailto:DGREVE@mgh.harvard.edu> Sent: Friday, May 10, 2019 3:27:15 PM To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spatial scale bar question In freeview, it is just an icon above the image window. Click on it and it should give you a scale bar

On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:
  Dear Freesurfers 

  Hi


  I am trying to add a spatial scale bar to my cortical maps in tksurfer. However,
  as it's mentioned in Freesurfer forum before, the scale bar in tksurfer shrinks
  when you zoom in the brain.

  I couldn't find a scale bar option in Freeview neither.

  I appreciate if you could let me know how to get a scale bar.


  Thanks

  Mona
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Nasiriavanaki, Zahra

10:49 a.m.

Thanks so much.

Zahra (Mona) Nasiriavanaki

Postdoctoral Research Fellow

Martinos Center for Biomedical Imaging

Massachusetts General Hospital

149 13th Street, 149-2615

Charlestown, MA, USA, 02129

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Ruopeng Wang rpwang@nmr.mgh.harvard.edu Sent: Friday, August 16, 2019 10:42:08 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spatial scale bar question

The 3D scale is also a 3d object in the view. When you zoom the view, the scale will also zoom. But the number should not change.

On Aug 16, 2019, at 10:25 AM, Nasiriavanaki, Zahra <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> wrote:

Hi Ruopeng

Thanks for your reply. I have a question though. When I zoom in the 3D image, the scale bar numbers don't change. Shouldn't they change when I zoom in?

Thanks Mona

Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpwang@nmr.mgh.harvard.edumailto:rpwang@nmr.mgh.harvard.edu> Sent: Friday, August 16, 2019 8:46:57 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] spatial scale bar question

Hi Mona,

If you are running the latest dev build, you can right click in the 3D view and choose “Show 3D scale”. The scale bars can only be placed at the boundary of the FOV.

Best, Ruopeng

On Aug 15, 2019, at 4:30 PM, Nasiriavanaki, Zahra <ZNASIRIAVANAKI@mgh.harvard.edumailto:ZNASIRIAVANAKI@mgh.harvard.edu> wrote:

Hi Freesurfer experts

I wanted to follow up on my question about "spatial scale bar" for significancy maps in FS. I appreciate if you let me know about the updates on that.

Thanks Mona

Zahra (Mona) Nasiriavanaki Postdoctoral Research Fellow Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129

Hi Mona

sure. As I said it is a bit more complicated than it seems. Ruopeng will post a note when something usable is in the dev version

Bruce

On Mon, 13 May 2019, Nasiriavanaki, Zahra wrote:

...

Yes Bruce.

It doesn't work.

I appreciate if you could let me know when you had any updates on it.

Thanks

Mona

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fischl@nmr.mgh.harvard.edumailto:fischl@nmr.mgh.harvard.edu> Sent: Friday, May 10, 2019 6:15:05 PM To: Freesurfer support list Subject: Re: [Freesurfer] spatial scale bar question I don't think it currently works in 3D mode as it is not trivial due to perspective transforms. Ruopeng is trying some things On Fri, 10 May 2019, Greve, Douglas N.,Ph.D. wrote:

...
here is a pick of it https://gate.nmr.mgh.harvard.edu/safelinks/greve/fv.colorbar.gif

[fv.colorbar.gif]

...
On 5/10/2019 3:40 PM, Nasiriavanaki, Zahra wrote:
  Thanks for your reply.

  I have overlaid the significance map on an inflated brain, and I don't see the scale
  bar icon anywhere.

  tksurferfv fsaverage lh inflated -ov sig.nii.gz
_

...
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu> Sent: Friday, May 10, 2019 3:27:15 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] spatial scale bar question In freeview, it is just an icon above the image window. Click on it and it should give you a scale bar

On 5/10/2019 3:13 PM, Nasiriavanaki, Zahra wrote:
  Dear Freesurfers

  Hi


  I am trying to add a spatial scale bar to my cortical maps in tksurfer. However,
  as it's mentioned in Freesurfer forum before, the scale bar in tksurfer shrinks
  when you zoom in the brain.

  I couldn't find a scale bar option in Freeview neither.

  I appreciate if you could let me know how to get a scale bar.


  Thanks

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

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participants (4)

Bruce Fischl
Greve, Douglas N.,Ph.D.
Nasiriavanaki, Zahra
Ruopeng Wang