Re: [Freesurfer] Chunks of missing WM

2012-12-17 Thread Bruce Fischl 

Hi Deirdre

just copy the updated recon-all into $FREESURFER_HOME/bin and you should 
be all set


cheers
Bruce
On Mon, 17 Dec 2012, Deirdre O Shea wrote:


Hi,

I have experienced this problem before also.So I have downloaded the script you 
provided but as a non-programmer I am wondering
how I can incorporate this script into my work using Linux. Can I simply copy 
and paste this into the text editer and run it
that way?

Thanks,
Deirdre

On Fri, Dec 14, 2012 at 4:37 PM, Bruce Fischl  
wrote:
  it doesn't, although the 5.2 mri_normalize should help as well

  cheers
  Bruce
  On Fri, 14 Dec 2012, Jonathan Holt wrote:

OK this is great. Does this require the latest version of 
Freesurfer? I see
recon-all v 5.2, we're running Freesurfer 5.0.0 for reference
On Dec 14, 2012, at 1:16 PM, Alex Hanganu wrote:

      I think Emily is talking about this one:

      
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/

      a.


      Le 14/12/2012 12:59 PM, Jonathan Holt a écrit :
      Emily,
This is good news, can I find or download this revised version
somewhere?

jon
On Dec 14, 2012, at 11:37 AM, Emily Rogalski wrote:

      We ran into this issue frequently and found that it
      was resolved by using the revised recon -all script
      that alters the stage where control points are
      considered.

      Emily


      On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt
       wrote:
            OK will do... I'll upload both versions,
            before and after recon-all ran. I am
            beginning to think it's an issue with
            the script that I am running... I'm
            looking at another brain and there are
            areas I did not touch at all where white
            matter voxels are being added or
            removed...


            On Dec 12, 2012, at 11:33 AM, Bruce
            Fischl wrote:

            > Hi Jon
            >
            > if you upload this subject we'll take
            a look
            > Bruce
            >
            >
            > On Wed, 12 Dec 2012, Jonathan Holt
            wrote:
            >
            >> I've had this happen a handful of
            times and I'm wondering what I can do
            about it. For reference using Freesurfer
            5.0.0.
            >>
            >> Edited a brain and ran "recon-all
            -autorecon2 -autorecon3 -s subj_id"
            which completed without error. The
            resulting brain had chunks of missing
            auxiliary volume in areas that I had not
            touched at all. This is bizarre and I am
            not sure what to do about it. Images of
            said issue attached of both main and
            auxiliary volumes.
            >>
            >>
            > 


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The inf

Re: [Freesurfer] Chunks of missing WM

2012-12-17 Thread Deirdre O Shea 
Hi,

I have experienced this problem before also.So I have downloaded the script
you provided but as a non-programmer I am wondering how I can incorporate
this script into my work using Linux. Can I simply copy and paste this into
the text editer and run it that way?

Thanks,
Deirdre

On Fri, Dec 14, 2012 at 4:37 PM, Bruce Fischl wrote:

> it doesn't, although the 5.2 mri_normalize should help as well
>
> cheers
> Bruce
>
> On Fri, 14 Dec 2012, Jonathan Holt wrote:
>
>  OK this is great. Does this require the latest version of Freesurfer? I
>> see
>> recon-all v 5.2, we're running Freesurfer 5.0.0 for reference
>> On Dec 14, 2012, at 1:16 PM, Alex Hanganu wrote:
>>
>>   I think Emily is talking about this one:
>>
>>   ftp://surfer.nmr.mgh.harvard.**edu/pub/dist/freesurfer/misc/**
>> allplatforms/
>>
>>   a.
>>
>>
>>   Le 14/12/2012 12:59 PM, Jonathan Holt a écrit :
>>   Emily,
>> This is good news, can I find or download this revised version
>> somewhere?
>>
>> jon
>> On Dec 14, 2012, at 11:37 AM, Emily Rogalski wrote:
>>
>>   We ran into this issue frequently and found that it
>>   was resolved by using the revised recon -all script
>>   that alters the stage where control points are
>>   considered.
>>
>>   Emily
>>
>>
>>   On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt
>>wrote:
>> OK will do... I'll upload both versions,
>> before and after recon-all ran. I am
>> beginning to think it's an issue with
>> the script that I am running... I'm
>> looking at another brain and there are
>> areas I did not touch at all where white
>> matter voxels are being added or
>> removed...
>>
>>
>> On Dec 12, 2012, at 11:33 AM, Bruce
>> Fischl wrote:
>>
>> > Hi Jon
>> >
>> > if you upload this subject we'll take
>> a look
>> > Bruce
>> >
>> >
>> > On Wed, 12 Dec 2012, Jonathan Holt
>> wrote:
>> >
>> >> I've had this happen a handful of
>> times and I'm wondering what I can do
>> about it. For reference using Freesurfer
>> 5.0.0.
>> >>
>> >> Edited a brain and ran "recon-all
>> -autorecon2 -autorecon3 -s subj_id"
>> which completed without error. The
>> resulting brain had chunks of missing
>> auxiliary volume in areas that I had not
>> touched at all. This is bizarre and I am
>> not sure what to do about it. Images of
>> said issue attached of both main and
>> auxiliary volumes.
>> >>
>> >>
>> >
>>
>>
>> __**_
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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
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>>  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] Chunks of missing WM

2012-12-14 Thread Bruce Fischl 

it doesn't, although the 5.2 mri_normalize should help as well

cheers
Bruce
On Fri, 14 
Dec 2012, Jonathan Holt wrote:



OK this is great. Does this require the latest version of Freesurfer? I see
recon-all v 5.2, we're running Freesurfer 5.0.0 for reference
On Dec 14, 2012, at 1:16 PM, Alex Hanganu wrote:

  I think Emily is talking about this one:

  ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/

  a.


  Le 14/12/2012 12:59 PM, Jonathan Holt a écrit :
  Emily,
This is good news, can I find or download this revised version
somewhere?

jon
On Dec 14, 2012, at 11:37 AM, Emily Rogalski wrote:

  We ran into this issue frequently and found that it
  was resolved by using the revised recon -all script
  that alters the stage where control points are
  considered.

  Emily


  On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt
   wrote:
OK will do... I'll upload both versions,
before and after recon-all ran. I am
beginning to think it's an issue with
the script that I am running... I'm
looking at another brain and there are
areas I did not touch at all where white
matter voxels are being added or
removed...


On Dec 12, 2012, at 11:33 AM, Bruce
Fischl wrote:

> Hi Jon
>
> if you upload this subject we'll take
a look
> Bruce
>
>
> On Wed, 12 Dec 2012, Jonathan Holt
wrote:
>
>> I've had this happen a handful of
times and I'm wondering what I can do
about it. For reference using Freesurfer
5.0.0.
>>
>> Edited a brain and ran "recon-all
-autorecon2 -autorecon3 -s subj_id"
which completed without error. The
resulting brain had chunks of missing
auxiliary volume in areas that I had not
touched at all. This is bizarre and I am
not sure what to do about it. Images of
said issue attached of both main and
auxiliary volumes.
>>
>>
> 


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Re: [Freesurfer] Chunks of missing WM

2012-12-14 Thread Jonathan Holt 
OK this is great. Does this require the latest version of Freesurfer? I see 
recon-all v 5.2, we're running Freesurfer 5.0.0 for reference
On Dec 14, 2012, at 1:16 PM, Alex Hanganu wrote:

> I think Emily is talking about this one:
> 
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/
> 
> a.
> 
> 
> Le 14/12/2012 12:59 PM, Jonathan Holt a écrit :
>> Emily,
>> 
>> This is good news, can I find or download this revised version somewhere?
>> 
>> jon
>> On Dec 14, 2012, at 11:37 AM, Emily Rogalski wrote:
>> 
>>> We ran into this issue frequently and found that it was resolved by using 
>>> the revised recon -all script that alters the stage where control points 
>>> are considered.
>>> 
>>> Emily
>>> 
>>> 
>>> On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt  wrote:
>>> OK will do... I'll upload both versions, before and after recon-all ran. I 
>>> am beginning to think it's an issue with the script that I am running... 
>>> I'm looking at another brain and there are areas I did not touch at all 
>>> where white matter voxels are being added or removed...
>>> 
>>> 
>>> On Dec 12, 2012, at 11:33 AM, Bruce Fischl wrote:
>>> 
>>> > Hi Jon
>>> >
>>> > if you upload this subject we'll take a look
>>> > Bruce
>>> >
>>> >
>>> > On Wed, 12 Dec 2012, Jonathan Holt wrote:
>>> >
>>> >> I've had this happen a handful of times and I'm wondering what I can do 
>>> >> about it. For reference using Freesurfer 5.0.0.
>>> >>
>>> >> Edited a brain and ran "recon-all -autorecon2 -autorecon3 -s subj_id" 
>>> >> which completed without error. The resulting brain had chunks of missing 
>>> >> auxiliary volume in areas that I had not touched at all. This is bizarre 
>>> >> and I am not sure what to do about it. Images of said issue attached of 
>>> >> both main and auxiliary volumes.
>>> >>
>>> >>
>>> > 
> 
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Re: [Freesurfer] Chunks of missing WM

2012-12-14 Thread Alex Hanganu 

I think Emily is talking about this one:

ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/

a.


Le 14/12/2012 12:59 PM, Jonathan Holt a écrit :

Emily,

This is good news, can I find or download this revised version somewhere?

jon
On Dec 14, 2012, at 11:37 AM, Emily Rogalski wrote:

We ran into this issue frequently and found that it was resolved by 
using the revised recon -all script that alters the stage where 
control points are considered.


Emily


On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt > wrote:


OK will do... I'll upload both versions, before and after
recon-all ran. I am beginning to think it's an issue with the
script that I am running... I'm looking at another brain and
there are areas I did not touch at all where white matter voxels
are being added or removed...


On Dec 12, 2012, at 11:33 AM, Bruce Fischl wrote:

> Hi Jon
>
> if you upload this subject we'll take a look
> Bruce
>
>
> On Wed, 12 Dec 2012, Jonathan Holt wrote:
>
>> I've had this happen a handful of times and I'm wondering what
I can do about it. For reference using Freesurfer 5.0.0.
>>
>> Edited a brain and ran "recon-all -autorecon2 -autorecon3 -s
subj_id" which completed without error. The resulting brain had
chunks of missing auxiliary volume in areas that I had not
touched at all. This is bizarre and I am not sure what to do
about it. Images of said issue attached of both main and
auxiliary volumes.
>>
>>
>



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Re: [Freesurfer] Chunks of missing WM

2012-12-14 Thread Jonathan Holt 
Emily,

This is good news, can I find or download this revised version somewhere?

jon
On Dec 14, 2012, at 11:37 AM, Emily Rogalski wrote:

> We ran into this issue frequently and found that it was resolved by using the 
> revised recon -all script that alters the stage where control points are 
> considered.
> 
> Emily
> 
> 
> On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt  wrote:
> OK will do... I'll upload both versions, before and after recon-all ran. I am 
> beginning to think it's an issue with the script that I am running... I'm 
> looking at another brain and there are areas I did not touch at all where 
> white matter voxels are being added or removed...
> 
> 
> On Dec 12, 2012, at 11:33 AM, Bruce Fischl wrote:
> 
> > Hi Jon
> >
> > if you upload this subject we'll take a look
> > Bruce
> >
> >
> > On Wed, 12 Dec 2012, Jonathan Holt wrote:
> >
> >> I've had this happen a handful of times and I'm wondering what I can do 
> >> about it. For reference using Freesurfer 5.0.0.
> >>
> >> Edited a brain and ran "recon-all -autorecon2 -autorecon3 -s subj_id" 
> >> which completed without error. The resulting brain had chunks of missing 
> >> auxiliary volume in areas that I had not touched at all. This is bizarre 
> >> and I am not sure what to do about it. Images of said issue attached of 
> >> both main and auxiliary volumes.
> >>
> >>
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> > 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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> 
> 
> 
> -- 
> Emily J Rogalski, PhD
> Assistant Research Professor
> Northwestern University
> Cognitive Neurology and Alzheimer's Disease Center (CNADC)
> 320 E Superior Street
> Searle Building 11th Floor
> Chicago, IL 60611
> 312-503-1155 phone
> 312-908-8789 fax
> erogal...@gmail.com
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> 
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> 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 
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Re: [Freesurfer] Chunks of missing WM

2012-12-14 Thread Emily Rogalski 
We ran into this issue frequently and found that it was resolved by using
the revised recon -all script that alters the stage where control points
are considered.

Emily


On Wed, Dec 12, 2012 at 10:42 AM, Jonathan Holt  wrote:

> OK will do... I'll upload both versions, before and after recon-all ran. I
> am beginning to think it's an issue with the script that I am running...
> I'm looking at another brain and there are areas I did not touch at all
> where white matter voxels are being added or removed...
>
>
> On Dec 12, 2012, at 11:33 AM, Bruce Fischl wrote:
>
> > Hi Jon
> >
> > if you upload this subject we'll take a look
> > Bruce
> >
> >
> > On Wed, 12 Dec 2012, Jonathan Holt wrote:
> >
> >> I've had this happen a handful of times and I'm wondering what I can do
> about it. For reference using Freesurfer 5.0.0.
> >>
> >> Edited a brain and ran "recon-all -autorecon2 -autorecon3 -s subj_id"
> which completed without error. The resulting brain had chunks of missing
> auxiliary volume in areas that I had not touched at all. This is bizarre
> and I am not sure what to do about it. Images of said issue attached of
> both main and auxiliary volumes.
> >>
> >>
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
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> 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
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> in error
> > but does not contain patient information, please contact the sender and
> properly
> > dispose of the e-mail.
> >
> >
> >
>
>
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-- 
Emily J Rogalski, PhD
Assistant Research Professor
Northwestern University
Cognitive Neurology and Alzheimer's Disease Center (CNADC)
320 E Superior Street
Searle Building 11th Floor
Chicago, IL 60611
312-503-1155 phone
312-908-8789 fax
erogal...@gmail.com
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Re: [Freesurfer] Chunks of missing WM

2012-12-12 Thread Jonathan Holt 
OK will do... I'll upload both versions, before and after recon-all ran. I am 
beginning to think it's an issue with the script that I am running... I'm 
looking at another brain and there are areas I did not touch at all where white 
matter voxels are being added or removed...


On Dec 12, 2012, at 11:33 AM, Bruce Fischl wrote:

> Hi Jon
> 
> if you upload this subject we'll take a look
> Bruce
> 
> 
> On Wed, 12 Dec 2012, Jonathan Holt wrote:
> 
>> I've had this happen a handful of times and I'm wondering what I can do 
>> about it. For reference using Freesurfer 5.0.0.
>> 
>> Edited a brain and ran "recon-all -autorecon2 -autorecon3 -s subj_id" which 
>> completed without error. The resulting brain had chunks of missing auxiliary 
>> volume in areas that I had not touched at all. This is bizarre and I am not 
>> sure what to do about it. Images of said issue attached of both main and 
>> auxiliary volumes.
>> 
>> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> 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] Chunks of missing WM

2012-12-12 Thread Bruce Fischl 
Hi Jon

if you upload this subject we'll take a look
Bruce


On Wed, 12 Dec 2012, Jonathan Holt wrote:

> I've had this happen a handful of times and I'm wondering what I can do about 
> it. For reference using Freesurfer 5.0.0.
>
> Edited a brain and ran "recon-all -autorecon2 -autorecon3 -s subj_id" which 
> completed without error. The resulting brain had chunks of missing auxiliary 
> volume in areas that I had not touched at all. This is bizarre and I am not 
> sure what to do about it. Images of said issue attached of both main and 
> auxiliary volumes.
>
>
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