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Today's Topics:

   1. no recon button (Burke,Sarah E)
   2. Brainstem segmentation (Haque, Muhammad E)
   3. Re: import ROI analysis results from Matlab into FreeSurfer
      (Bruce Fischl)
   4. Re: no recon button (Douglas Greve)
   5. Re: no recon button (Burke,Sarah E)
   6. Re: no recon button (Douglas Greve)
   7. Re: no recon button (Burke,Sarah E)


----------------------------------------------------------------------

Message: 1
Date: Mon, 2 May 2016 16:14:28 +0000
From: "Burke,Sarah E" <saraheburke@ufl.edu>
Subject: [Freesurfer] no recon button
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BLUPR0801MB155544A9C1E2604C95B3B8DCB8790@BLUPR0801MB1555.namprd08.prod.outlook.com>

Content-Type: text/plain; charset="iso-8859-1"

Hello,


I searched the mail list and saw that others have had this problem, but I see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for Linux.  I have no recon button. What should I do?


Thank you
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Message: 2
Date: Mon, 2 May 2016 16:24:48 +0000
From: "Haque, Muhammad E" <Muhammad.E.Haque@uth.tmc.edu>
Subject: [Freesurfer] Brainstem segmentation
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <219F72CE2687D945A3D729188FF8DB8227C473AD@UTHMAIL3.uthouston.edu>
Content-Type: text/plain; charset="us-ascii"

Dear FreeSurfer Users,



I would like to know if we can do brainstem segmentation as described in the
recent publication

http://www.sciencedirect.com/science/article/pii/S1053811915001895



Author as well as FreeSurfer website mention that this feature is only
available in FreeSurfer 6.0 and later version



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



Where I can download this FreeSurfer 6.0?



Thanks.



Haque

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Message: 3
Date: Mon, 2 May 2016 12:57:10 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] import ROI analysis results from Matlab into
        FreeSurfer
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <alpine.LRH.2.20.1605021255520.27719@gate.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-15"

Hi Domenico

check out read_annotation.m and write_annotation.m. YOu should be able to
create your own .annot file and write it out from matlab to be displayed
in freeeview.

cheers
Bruce

On Mon, 2 May 2016,
Domenico Zac? wrote:

> Dear FS experts,
>
> I dumped the average cortical thickness values of 68 ROI using
> aparcstats2table into a spreadsheet, then generated a set of CT networks
> measures in matlab for each ROI. Now how can I visualize the results back in
> FreeSurfer?
>
> Thanks
>
> Domenico Zac?, PhD
>
>
> MR Lab Research Fellow
>
> Center for Mind/Brain Sciences
>
> University of Trento, Italy
>
> Via delle Regole, 101
>
> 38100 Mattarello (TN)
>
> Italy
>
> ?
>
> Telephone:?+39-0461-28 3069
> Fax:?+39-0461-28-3066
>
> Email:?domenico.zaca@unitn.it
>
> MRI Methods Group:?http://r.unitn.it/en/cimec/mri
>
>
>

------------------------------

Message: 4
Date: Mon, 2 May 2016 13:29:24 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] no recon button
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <57278E74.8020807@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

freeview does not have a recon button. You have to run recon-all from
the command line.

On 5/2/16 12:14 PM, Burke,Sarah E wrote:
>
> Hello,
>
>
> I searched the mail list and saw that others have had this problem,
> but I see no answers to their queries. I have version 1.0 (5/13/2013)
> of Freeview for Linux.  I have no recon button. What should I do?
>
>
> Thank you
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Message: 5
Date: Mon, 2 May 2016 17:44:42 +0000
From: "Burke,Sarah E" <saraheburke@ufl.edu>
Subject: Re: [Freesurfer] no recon button
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BLUPR0801MB15559B407AB74E3B4D9ADABDB8790@BLUPR0801MB1555.namprd08.prod.outlook.com>

Content-Type: text/plain; charset="iso-8859-1"

Thank you Douglas. However, in the tutorial for editing output, it says to use the recon edit button to manually perform edits. After this step, I use the command line and recon-all. How do I do the manual edits without this button. I do see a voxel edit button.

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview

[https://surfer.nmr.mgh.harvard.edu/wiki/fswiki_htdocs/common/fslogosmall.png]<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview>

FsTutorial/PialEdits_freeview - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview>
surfer.nmr.mgh.harvard.edu
top | previous Correcting Pial Surfaces. To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to ...




________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve <greve@nmr.mgh.harvard.edu>
Sent: Monday, May 2, 2016 1:29 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] no recon button

freeview does not have a recon button. You have to run recon-all from the command line.

On 5/2/16 12:14 PM, Burke,Sarah E wrote:

Hello,


I searched the mail list and saw that others have had this problem, but I see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for Linux.  I have no recon button. What should I do?


Thank you



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

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Message: 6
Date: Mon, 2 May 2016 14:31:03 -0400
From: Douglas Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] no recon button
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <57279CE7.50102@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

Can you send a snapshot of your Freeview window? The Recon Edit button
looks like a sagittal slice with an "R" in it and a pencil pointing to it.

On 5/2/16 1:44 PM, Burke,Sarah E wrote:
>
> Thank you Douglas. However, in the tutorial for editing output, it
> says to use the recon edit button to manually perform edits. After
> this step, I use the command line and recon-all. How do I do the
> manual edits without this button. I do see a voxel edit button.
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview
>
> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview>
>
> FsTutorial/PialEdits_freeview - Free Surfer Wiki
> <https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview>
> surfer.nmr.mgh.harvard.edu
> top | previous Correcting Pial Surfaces. To follow this exercise
> exactly be sure you've downloaded the tutorial data set before you
> begin. If you choose not to ...
>
>
>
>
> ------------------------------------------------------------------------
> *From:* freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve
> <greve@nmr.mgh.harvard.edu>
> *Sent:* Monday, May 2, 2016 1:29 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] no recon button
> freeview does not have a recon button. You have to run recon-all from
> the command line.
>
> On 5/2/16 12:14 PM, Burke,Sarah E wrote:
>>
>> Hello,
>>
>>
>> I searched the mail list and saw that others have had this problem,
>> but I see no answers to their queries. I have version 1.0 (5/13/2013)
>> of Freeview for Linux.  I have no recon button. What should I do?
>>
>>
>> Thank you
>>
>>
>>
>> _______________________________________________
>> 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

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Message: 7
Date: Mon, 2 May 2016 18:58:15 +0000
From: "Burke,Sarah E" <saraheburke@ufl.edu>
Subject: Re: [Freesurfer] no recon button
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <BLUPR0801MB155564C7E5336D1DE091DD60B8790@BLUPR0801MB1555.namprd08.prod.outlook.com>

Content-Type: text/plain; charset="iso-8859-1"




________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve <greve@nmr.mgh.harvard.edu>
Sent: Monday, May 2, 2016 2:31 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] no recon button

Can you send a snapshot of your Freeview window? The Recon Edit button looks like a sagittal slice with an "R" in it and a pencil pointing to it.

On 5/2/16 1:44 PM, Burke,Sarah E wrote:

Thank you Douglas. However, in the tutorial for editing output, it says to use the recon edit button to manually perform edits. After this step, I use the command line and recon-all. How do I do the manual edits without this button. I do see a voxel edit button.

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview

[https://surfer.nmr.mgh.harvard.edu/wiki/fswiki_htdocs/common/fslogosmall.png]<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview>

FsTutorial/PialEdits_freeview - Free Surfer Wiki<https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits_freeview>
surfer.nmr.mgh.harvard.edu
top | previous Correcting Pial Surfaces. To follow this exercise exactly be sure you've downloaded the tutorial data set before you begin. If you choose not to ...




________________________________
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 Douglas Greve <greve@nmr.mgh.harvard.edu><mailto:greve@nmr.mgh.harvard.edu>
Sent: Monday, May 2, 2016 1:29 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] no recon button

freeview does not have a recon button. You have to run recon-all from the command line.

On 5/2/16 12:14 PM, Burke,Sarah E wrote:

Hello,


I searched the mail list and saw that others have had this problem, but I see no answers to their queries. I have version 1.0 (5/13/2013) of Freeview for Linux.  I have no recon button. What should I do?


Thank you



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




_______________________________________________
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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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End of Freesurfer Digest, Vol 147, Issue 4
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