Re: [Freesurfer] Wm correction

[Bruce Fischl]

sure, let us know after you have uploaded it.

Bruce
On Fri, 29 Jan 2016, maryam 
koochaki wrote:



Thanks, I also have another major problem with the subjects I am working on.
Two of the subjects intend to freeze at #@# Fix Topology rh step while
running reconstruction process.
CORRECTING DEFECT 12 (vertices=29993, convex hull=7603)

I will upload one of the subjects to your ftp site, if you could take a look
to see what is the defect.
Really appreciate your help in advance,

Maryam
 






Regards,
Maryam Kouchakidivkolaei




On Thursday, January 28, 2016 5:51 PM, Bruce Fischl
 wrote:


Hi Maryam
We are working hard to get it out, but it's not quite ready yet. We will
make an announcement when we have a beta version
Bruce

On Jan 28, 2016, at 8:25 PM, maryam koochaki 
wrote:

  Hi Bruce,
How can I download version 6?


Best,
Maryam
 






Regards,
Maryam Kouchakidivkolaei


On Thursday, January 28, 2016 5:55 AM, Bruce Fischl
 wrote:


Hi Maryam

have you look at the aseg? I suspect that it didn't properly handle
the
very large ventricles in this subject. Try manually editing it. V6
handles this kind of thing significantly better

cheers
Bruce
On Thu, 28 Jan 2016, maryam
koochaki wrote:

> Hi Bruce,
> I am editing a brain with Freesurfer version 5.3. I have a issue in
Lateral
> Ventricle. As you can see in the image attached, the big part is
excluded in
> both hemisphere. I tried to fill it by editing wm volume but the
problem
> still exists.
> Do you have any suggestion?
> Thanks,
> Maryam
>  
>
>
>
>
>
>
>
>
>

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Re: [Freesurfer] Wm correction

[maryam koochaki]

Hi Bruce,I uploaded yesterday.
best,
Maryam
 





Regards,Maryam Kouchakidivkolaei 

On Friday, January 29, 2016 5:47 AM, Bruce Fischl 
 wrote:
 

 sure, let us know after you have uploaded it.

Bruce
On Fri, 29 Jan 2016, maryam 
koochaki wrote:

> Thanks, I also have another major problem with the subjects I am working on.
> Two of the subjects intend to freeze at #@# Fix Topology rh step while
> running reconstruction process.
> CORRECTING DEFECT 12 (vertices=29993, convex hull=7603)
> 
> I will upload one of the subjects to your ftp site, if you could take a look
> to see what is the defect.
> Really appreciate your help in advance,
> 
> Maryam
>  
> 
> 
> 
> 
> 
> 
> Regards,
> Maryam Kouchakidivkolaei
> 
> 
> 
> 
> On Thursday, January 28, 2016 5:51 PM, Bruce Fischl
>  wrote:
> 
> 
> Hi Maryam
> We are working hard to get it out, but it's not quite ready yet. We will
> make an announcement when we have a beta version
> Bruce
> 
> On Jan 28, 2016, at 8:25 PM, maryam koochaki 
> wrote:
>
>      Hi Bruce,
> How can I download version 6?
> 
> 
> Best,
> Maryam
>  
> 
> 
> 
> 
> 
> 
> Regards,
> Maryam Kouchakidivkolaei
> 
> 
> On Thursday, January 28, 2016 5:55 AM, Bruce Fischl
>  wrote:
> 
> 
> Hi Maryam
> 
> have you look at the aseg? I suspect that it didn't properly handle
> the
> very large ventricles in this subject. Try manually editing it. V6
> handles this kind of thing significantly better
> 
> cheers
> Bruce
> On Thu, 28 Jan 2016, maryam
> koochaki wrote:
> 
> > Hi Bruce,
> > I am editing a brain with Freesurfer version 5.3. I have a issue in
> Lateral
> > Ventricle. As you can see in the image attached, the big part is
> excluded in
> > both hemisphere. I tried to fill it by editing wm volume but the
> problem
> > still exists.
> > Do you have any suggestion?
> > Thanks,
> > Maryam
> >  
> >
> >
> >
> >
> >
> >
> >
> >
> >
> 
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> it is
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> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you
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> and properly
> dispose of the e-mail.
> 
>
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Re: [Freesurfer] Wm correction

[maryam koochaki]

Hi Bruce,Thanks for your reply, I will take look on aseg volume.
Best,Mrayam
 






 

On Thursday, January 28, 2016 5:55 AM, Bruce Fischl 
 wrote:
 

 Hi Maryam

have you look at the aseg? I suspect that it didn't properly handle the 
very large ventricles in this subject. Try manually editing it. V6 
handles this kind of thing significantly better

cheers
Bruce
On Thu, 28 Jan 2016, maryam 
koochaki wrote:

> Hi Bruce,
> I am editing a brain with Freesurfer version 5.3. I have a issue in Lateral
> Ventricle. As you can see in the image attached, the big part is excluded in
> both hemisphere. I tried to fill it by editing wm volume but the problem
> still exists.
> Do you have any suggestion?
> Thanks,
> Maryam
>  
> 
> 
> 
> 
> 
> 
> 
> 
>
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Re: [Freesurfer] Wm correction

[maryam koochaki]

Hi Bruce,
How can I download version 6?

Best,Maryam
 





Regards,Maryam Kouchakidivkolaei 

On Thursday, January 28, 2016 5:55 AM, Bruce Fischl 
 wrote:
 

 Hi Maryam

have you look at the aseg? I suspect that it didn't properly handle the 
very large ventricles in this subject. Try manually editing it. V6 
handles this kind of thing significantly better

cheers
Bruce
On Thu, 28 Jan 2016, maryam 
koochaki wrote:

> Hi Bruce,
> I am editing a brain with Freesurfer version 5.3. I have a issue in Lateral
> Ventricle. As you can see in the image attached, the big part is excluded in
> both hemisphere. I tried to fill it by editing wm volume but the problem
> still exists.
> Do you have any suggestion?
> Thanks,
> Maryam
>  
> 
> 
> 
> 
> 
> 
> 
> 
>
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Re: [Freesurfer] Wm correction

[maryam koochaki]

Thanks, I also have another major problem with the subjects I am working on.Two 
of the subjects intend to freeze at #@# Fix Topology rh step while running 
reconstruction process.
 CORRECTING DEFECT 12 (vertices=29993, convex hull=7603)
I will upload one of the subjects to your ftp site, if you could take a look to 
see what is the defect.
Really appreciate your help in advance,
Maryam
 





Regards,Maryam Kouchakidivkolaei 

   

 On Thursday, January 28, 2016 5:51 PM, Bruce Fischl 
 wrote:
 

 Hi MaryamWe are working hard to get it out, but it's not quite ready yet. We 
will make an announcement when we have a beta versionBruce
On Jan 28, 2016, at 8:25 PM, maryam koochaki  wrote:


Hi Bruce,
How can I download version 6?

Best,Maryam
 





Regards,Maryam Kouchakidivkolaei 

On Thursday, January 28, 2016 5:55 AM, Bruce Fischl 
 wrote:
 

 Hi Maryam

have you look at the aseg? I suspect that it didn't properly handle the 
very large ventricles in this subject. Try manually editing it. V6 
handles this kind of thing significantly better

cheers
Bruce
On Thu, 28 Jan 2016, maryam 
koochaki wrote:

> Hi Bruce,
> I am editing a brain with Freesurfer version 5.3. I have a issue in Lateral
> Ventricle. As you can see in the image attached, the big part is excluded in
> both hemisphere. I tried to fill it by editing wm volume but the problem
> still exists.
> Do you have any suggestion?
> Thanks,
> Maryam
>  
> 
> 
> 
> 
> 
> 
> 
> 
>
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Re: [Freesurfer] Wm correction

[Bruce Fischl]

Hi Maryam
We are working hard to get it out, but it's not quite ready yet. We will make 
an announcement when we have a beta version
Bruce

> On Jan 28, 2016, at 8:25 PM, maryam koochaki  
> wrote:
> 
> Hi Bruce,
> How can I download version 6?
> 
> 
> Best,
> Maryam
>  
> 
> 
> 
> 
> 
> 
> Regards,
> Maryam Kouchakidivkolaei
> 
> 
> On Thursday, January 28, 2016 5:55 AM, Bruce Fischl 
>  wrote:
> 
> 
> Hi Maryam
> 
> have you look at the aseg? I suspect that it didn't properly handle the 
> very large ventricles in this subject. Try manually editing it. V6 
> handles this kind of thing significantly better
> 
> cheers
> Bruce
> 
> On Thu, 28 Jan 2016, maryam 
> koochaki wrote:
> 
> > Hi Bruce,
> > I am editing a brain with Freesurfer version 5.3. I have a issue in Lateral
> > Ventricle. As you can see in the image attached, the big part is excluded in
> > both hemisphere. I tried to fill it by editing wm volume but the problem
> > still exists.
> > Do you have any suggestion?
> > Thanks,
> > Maryam
> >  
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> > 
> >
> 
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> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
> 
> 
> 
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Re: [Freesurfer] Wm correction

[Bruce Fischl]

Hi Maryam

have you look at the aseg? I suspect that it didn't properly handle the 
very large ventricles in this subject. Try manually editing it. V6 
handles this kind of thing significantly better


cheers
Bruce
On Thu, 28 Jan 2016, maryam 
koochaki wrote:



Hi Bruce,
I am editing a brain with Freesurfer version 5.3. I have a issue in Lateral
Ventricle. As you can see in the image attached, the big part is excluded in
both hemisphere. I tried to fill it by editing wm volume but the problem
still exists.
Do you have any suggestion?
Thanks,
Maryam
 








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Re: [Freesurfer] wm correction issues

[Ilana Hairston]

Hi there.

 we have been doing some white matter corrections, based on the wiki
 instructions.  After filling in some missing voxels we ran ...autorecon2-wm
 autorecon3 ... but it doesn't look like the white matter was corrected.

 thanks
 ilana




-- 
***
Ilana Hairston ,PhD
Research Assistant Professor
4250 Plymouth Rd. (rm 2439)
Psychiatry Department, Addiction Research Center
University of Michigan, Ann Arbor MI 48109-2700
Tel: 734-232-0232; Mobile: 650-906-8449

Sentimental Insomnia and Nostalgia Disorders Sciences


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Re: [Freesurfer] wm correction issues

[Bruce Fischl]

Hi Ilana,

we need more information if we are to help you. What kind of corrections? 
What commands did you run? What did the output look like?

cheers
Bruce
On Fri, 21 May 
2010, Ilana Hairston wrote:

 Hi there.

 we have been doing some white matter corrections, based on the wiki
 instructions.  After filling in some missing voxels we ran ...autorecon2-wm
 autorecon3 ... but it doesn't look like the white matter was corrected.

 thanks
 ilana





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Re: [Freesurfer] wm correction issues

[Allison Stevens]

And what version of freesurfer are you using? 

On May 21, 2010, at 11:21 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote:

 Hi Ilana,
 
 we need more information if we are to help you. What kind of corrections? 
 What commands did you run? What did the output look like?
 
 cheers
 Bruce
 On Fri, 21 May 
 2010, Ilana Hairston wrote:
 
 Hi there.
 
 we have been doing some white matter corrections, based on the wiki
 instructions.  After filling in some missing voxels we ran ...autorecon2-wm
 autorecon3 ... but it doesn't look like the white matter was corrected.
 
 thanks
 ilana
 
 
 
 
 
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