Re: [Freesurfer] No labels file in label directory?

2014-02-26 Thread Douglas N Greve 
yep, you'll need a new version of mri_segstats, which you can find by 
following the thread that Louis posted
doug
On 02/26/2014 12:32 PM, Louis Nicholas Vinke wrote:
> Hi Sabin,
> What command did you run?  Sending the recon-all.log file in the 
> scripts dir might be a little more helpful.  It's failing because the 
> ribbon.mgz does not exist which requires surfaces.
>
> This thread might be relevant:
> http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32876.html 
>
>
> -Louis
>
> On Wed, 26 Feb 2014, sabin khadka wrote:
>
>> Hi Doug,
>> I tried running autorecon2 after successful autorecon1, however it 
>> crashed. I could not figure out why it crashed and how to fix it. Any 
>> suggestions.
>> I've attached log file of autorecon2
>>
>> -Sabin
>>
>>
>>
>> On Tuesday, February 25, 2014 10:47 AM, Douglas Greve 
>>  wrote:
>>
>> You did not run it all the way through (you stopped at autorecon2)
>> doug
>>
>>
>> On 2/25/14 9:00 AM, sabin khadka wrote:
>>
>> Thanks Doug. recon-all.log is attached herewith.
>>
>>
>>
>> On Monday, February 24, 2014 5:07 PM, Douglas N Greve 
>>  wrote:
>>
>> are you sure it did not fail? Can you post the recon-all.log file to the
>> list?
>>
>>
>> On 02/24/2014 04:22 PM, sabin khadka wrote:
>> > Hi all,
>> > I ran recon-all -all and all the subjects finished without any error.
>> > However in few subjects directory, labels sub-directory only have
>> > lh.cortex.label and rh.cortex.label and not other label files like
>> > *.label and *.annot. Could anyone help me on how to fix this.
>> >
>> > -Sabin
>>
>> >
>> >
>> >
>> > ___
>> > 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
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> 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.
>>
>>
>>
>>
>>
>> ___
>> 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.
>>
>>
>>
>>
>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] No labels file in label directory?

2014-02-26 Thread Louis Nicholas Vinke 
Hi Sabin,
What command did you run?  Sending the recon-all.log file in the scripts 
dir might be a little more helpful.  It's failing because the ribbon.mgz 
does not exist which requires surfaces.

This thread might be relevant:
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32876.html

-Louis

On Wed, 26 Feb 2014, sabin khadka wrote:

> Hi Doug,
> I tried running autorecon2 after successful autorecon1, however it crashed. I 
> could not figure out why it crashed and how to fix it. Any suggestions.
> I've attached log file of autorecon2
> 
> -Sabin
> 
> 
> 
> On Tuesday, February 25, 2014 10:47 AM, Douglas Greve 
>  wrote:
> 
> You did not run it all the way through (you stopped at autorecon2)
> doug
> 
> 
> On 2/25/14 9:00 AM, sabin khadka wrote:
> 
> Thanks Doug. recon-all.log is attached herewith.
> 
> 
> 
> On Monday, February 24, 2014 5:07 PM, Douglas N Greve 
>  wrote:
> 
> are you sure it did not fail? Can you post the recon-all.log file to the
> list?
> 
> 
> On 02/24/2014 04:22 PM, sabin khadka wrote:
> > Hi all,
> > I ran recon-all -all and all the subjects finished without any error.
> > However in few subjects directory, labels sub-directory only have
> > lh.cortex.label and rh.cortex.label and not other label files like
> > *.label and *.annot. Could anyone help me on how to fix this.
> >
> > -Sabin
> 
> >
> >
> >
> > ___
> > 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
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> ___
> 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.
> 
> 
> 
> 
> 
> ___
> 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] No labels file in label directory?

2014-02-25 Thread Douglas Greve 


You did not run it all the way through (you stopped at autorecon2)
doug


On 2/25/14 9:00 AM, sabin khadka wrote:

Thanks Doug. recon-all.log is attached herewith.



On Monday, February 24, 2014 5:07 PM, Douglas N Greve 
 wrote:


are you sure it did not fail? Can you post the recon-all.log file to the
list?


On 02/24/2014 04:22 PM, sabin khadka wrote:
> Hi all,
> I ran recon-all -all and all the subjects finished without any error.
> However in few subjects directory, labels sub-directory only have
> lh.cortex.label and rh.cortex.label and not other label files like
> *.label and *.annot. Could anyone help me on how to fix this.
>
> -Sabin

>
>
>
> ___
> 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
gr...@nmr.mgh.harvard.edu 
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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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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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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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] No labels file in label directory?

2014-02-24 Thread Douglas N Greve 

are you sure it did not fail? Can you post the recon-all.log file to the 
list?


On 02/24/2014 04:22 PM, sabin khadka wrote:
> Hi all,
> I ran recon-all -all and all the subjects finished without any error. 
> However in few subjects directory, labels sub-directory only have 
> lh.cortex.label and rh.cortex.label and not other label files like 
> *.label and *.annot. Could anyone help me on how to fix this.
>
> -Sabin
>
>
>
> ___
> 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
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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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.

[Freesurfer] No labels file in label directory?

2014-02-24 Thread sabin khadka 
Hi all,
I ran recon-all -all and all the subjects finished without any error. However 
in few subjects directory, labels sub-directory only have lh.cortex.label and 
rh.cortex.label and not other label files like *.label and *.annot. Could 
anyone help me on how to fix this.

-Sabin___
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.