subject:"\[Freesurfer\] Freesurfer\-Error message"

Re: [Freesurfer] Freesurfer-Error message

2012-09-05 Thread Bruce Fischl

Is that the actual name of the file? Does it have a dcm extension?
On Wed, 5 
Sep 2012, Varghese, Chikku wrote:

> Thanks Bruce,
> Still no luck,this  what I am getting
>
>
> /freesurfer/subjects/test1> recon-all -i 
> /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm -subjid test7 -all
> Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0
> Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0
> INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects
> Actual FREESURFER_HOME /home/virtualuser/freesurfer
> Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 
> 2009 i686 GNU/Linux
> /home/virtualuser/freesurfer/subjects/test7
>
> mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm 
> /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz
>
> mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm 
> /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz
> file not found or unknown file type for file 
> /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm
> Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 
> 2009 i686 GNU/Linux
>
> recon-all -s test7 exited with ERRORS at Wed Sep  5 09:51:17 EDT 2012
>
> For more details, see the log file 
> /home/virtualuser/freesurfer/subjects/test7/scripts/recon-all.log
> To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
> FreeSurfer:~/freesurfer/subjects/test1>
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Dienstag, 4. September 2012 18:25
> To: Varghese, Chikku
> Subject: Re: [Freesurfer] Freesurfer-Error message
>
> you need a -all at the end to tell it what to do. And please cc the list so 
> others can answer!
>
> On Tue, 4 Sep 2012, Varghese, Chikku wrote:
>
>>
>> recon-all -i
>> /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm -subjid
>> test4
>>
>> Is it this command I should use?
>>
>>
>>
>
>
> 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] Freesurfer-Error message

2012-09-05 Thread Varghese Chikku

Thanks Bruce,

Still no luck,this  what I am getting





/freesurfer/subjects/test1> recon-all -i
/media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm -subjid test7
-all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0

Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0

INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects

Actual FREESURFER_HOME /home/virtualuser/freesurfer Linux FreeSurfer
2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux

/home/virtualuser/freesurfer/subjects/test7



 mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm
/home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz



mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm
/home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz

file not found or unknown file type for file
/media/sf_freesurferstudys/raw/raw_scr/T1pre/Image1.dcm

Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC
2009 i686 GNU/Linux



recon-all -s test7 exited with ERRORS at Wed Sep  5 09:51:17 EDT 2012



For more details, see the log file
/home/virtualuser/freesurfer/subjects/test7/scripts/recon-all.log

To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



FreeSurfer:~/freesurfer/subjects/test1>


On 4 September 2012 14:37, Bruce Fischl  wrote:

> if that's the name of the image file. Can you post the list on your
> replies so others can answer?
>
> thanks
> Bruce
>
> On Tue, 4 Sep 2012, Varghese Chikku wrote:
>
> Hi Bruce,
>> Many thanks for  you mail.
>> Is this the  command  you referring to.
>> recon-all -i /media/sf_freesurferstudys/**raw/raw_scr/T1pre/Image1.**dcm
>> -subjid test4
>> Thanks
>> Chikku
>>
>> On 3 September 2012 17:33, Bruce Fischl 
>> wrote:
>>   Hi Chikku
>>
>>   you need to give it the path to an image file (any one will do) and
>> it will figure out the other slices that makeup
>>   the same series. What is the resolution of your data? 50 slices
>> isn't usually enough to cover the brain at high
>>   enough resolution to get good thickness results.
>>
>>   cheers
>>   Bruce
>>
>>
>>   On Mon, 3 Sep 2012, Varghese Chikku wrote:
>>
>>
>> Hi,
>>
>> While running the following command:
>>
>> recon-all -i /media/sf_freesurferstudys/**raw/raw_scr/T1pre
>> -subjid test2
>>
>> I keep seeing the following error:
>>
>> ...
>>
>> corRead(): can't open file
>> /media/sf_freesurferstudys/**raw/raw_scr/T1pre/COR-.info
>> $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
>> reading from /media/sf_freesurferstudys/**
>> raw/raw_scr/T1pre...
>> Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17
>> 01:57:59 UTC
>> 2009 i686 GNU/Linux
>> recon-all -s test2 exited with ERRORS at Fri Aug 31 04:20:28
>> EDT 2012
>>
>>
>> My image files, in dcm format, are at
>> /media/sf_freesurferstudys/**raw/raw_scr/T1pre :
>>
>> /media/sf_freesurferstudys/**raw/raw_scr/T1pre> ls
>> Image1  Image00010 Image00019  Image00028 Image00037
>> Image00046
>> Image2  Image00011 Image00020  Image00029 Image00038
>> Image00047
>> Image3  Image00012 Image00021  Image00030 Image00039
>> Image00048
>> Image4  Image00013 Image00022  Image00031 Image00040
>> Image00049
>> Image5  Image00014 Image00023  Image00032 Image00041
>> Image00050
>> Image6  Image00015 Image00024  Image00033 Image00042
>> Image7  Image00016 Image00025  Image00034 Image00043
>> Image8  Image00017 Image00026  Image00035 Image00044
>> Image9  Image00018 Image00027  Image00036 Image00045
>>
>>  Many thanks for  your help.
>> chikku
>>
>>
>>
>>
>> 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] Freesurfer-Error message

2012-09-03 Thread Bruce Fischl


Hi Chikku

you need to give it the path to an image file (any one will do) and it 
will figure out the other slices that makeup the same series. What is the 
resolution of your data? 50 slices isn't usually enough to cover the brain 
at high enough resolution to get good thickness results.


cheers
Bruce


On Mon, 3 Sep 2012, Varghese Chikku wrote:


 
Hi,
 
While running the following command:

recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre -subjid test2

I keep seeing the following error:

...

corRead(): can't open file
/media/sf_freesurferstudys/raw/raw_scr/T1pre/COR-.info
$Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
reading from /media/sf_freesurferstudys/raw/raw_scr/T1pre...
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC
2009 i686 GNU/Linux
recon-all -s test2 exited with ERRORS at Fri Aug 31 04:20:28 EDT 2012


My image files, in dcm format, are at
/media/sf_freesurferstudys/raw/raw_scr/T1pre :

/media/sf_freesurferstudys/raw/raw_scr/T1pre> ls
Image1  Image00010 Image00019  Image00028 Image00037  Image00046
Image2  Image00011 Image00020  Image00029 Image00038  Image00047
Image3  Image00012 Image00021  Image00030 Image00039  Image00048
Image4  Image00013 Image00022  Image00031 Image00040  Image00049
Image5  Image00014 Image00023  Image00032 Image00041  Image00050
Image6  Image00015 Image00024  Image00033 Image00042
Image7  Image00016 Image00025  Image00034 Image00043
Image8  Image00017 Image00026  Image00035 Image00044
Image9  Image00018 Image00027  Image00036 Image00045

 Many thanks for  your help.
chikku

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contains patient information, please contact the Partners Compliance HelpLine at
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[Freesurfer] Freesurfer-Error message

2012-09-03 Thread Varghese Chikku

Hi,

While running the following command:

recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre -subjid test2

I keep seeing the following error:

...

corRead(): can't open file
/media/sf_freesurferstudys/raw/raw_scr/T1pre/COR-.info
$Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $
reading from /media/sf_freesurferstudys/raw/raw_scr/T1pre...
Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC
2009 i686 GNU/Linux
recon-all -s test2 exited with ERRORS at Fri Aug 31 04:20:28 EDT 2012


My image files, in dcm format, are at
/media/sf_freesurferstudys/raw/raw_scr/T1pre :

/media/sf_freesurferstudys/raw/raw_scr/T1pre> ls
Image1  Image00010 Image00019  Image00028 Image00037  Image00046
Image2  Image00011 Image00020  Image00029 Image00038  Image00047
Image3  Image00012 Image00021  Image00030 Image00039  Image00048
Image4  Image00013 Image00022  Image00031 Image00040  Image00049
Image5  Image00014 Image00023  Image00032 Image00041  Image00050
Image6  Image00015 Image00024  Image00033 Image00042
Image7  Image00016 Image00025  Image00034 Image00043
Image8  Image00017 Image00026  Image00035 Image00044
Image9  Image00018 Image00027  Image00036 Image00045
 Many thanks for  your help.
chikku
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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] Freesurfer Error Message in running autorecon2 & autorecon3

2011-10-21 Thread Vy Dinh

Thank you for the info. I will try to redownload this version for the BA labels.

Vy T.U. Dinh
Research Assistant, Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: vy_d...@rush.edu


From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Friday, October 21, 2011 12:22 PM
To: Vy Dinh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
autorecon3

The BA labels should be in

$FREESURFER_HOME/subjects/fsaverage/label

doug
Vy Dinh wrote:
> 5.0
>
> Vy T.U. Dinh
> Research Assistant, Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853
> Fax: (312) 563-4660
> Email: vy_d...@rush.edu
>
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, October 21, 2011 9:51 AM
> To: Vy Dinh
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
> autorecon3
>
> So the BA labels don't exist in
> $FREESURFER_HOME/subjects/fsaverage/label? What version are you using?
> doug
>
> Vy Dinh wrote:
>
>> You're absolutely right. The lh.BA1.label file is missing within 
>> freesurfer/fsaverage. I thought that we may have had the same issue as this 
>> poster 
>> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19399.html) 
>> since we use a mount, but it seems that the missing BA labels is the real 
>> issue. My main concern, then, is how this has affected our processing 
>> (besides not running the BA labels) and whether any reruns would be 
>> necessary. In other words, did recon-all simply skip the BA labels and ran 
>> the other processes or did it crash midway?
>>
>> Also, if you have uploaded a fsaverage folder that contains these missing 
>> files, I will gladly download them from your site. Note that we had run the 
>> recon-all commands with Freesurfer version 5.0. This error was never 
>> encountered until recently (even though we had not upgraded to the newer 
>> version).
>>
>> Thank you for your time,
>>
>>
>> Vy T.U. Dinh
>> Research Assistant, Neurological Sciences
>> Rush University Medical Center
>> Phone: (312) 563-3853
>> Fax: (312) 563-4660
>> Email: vy_d...@rush.edu
>>
>> 
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, October 20, 2011 1:10 PM
>> To: Vy Dinh
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
>> autorecon3
>>
>> No, it means that it cannot find that file.
>> doug
>>
>> Vy Dinh wrote:
>>
>>
>>> Then does it mean that I can ignore this error message?
>>>
>>> Vy T.U. Dinh
>>> Research Assistant, Neurological Sciences
>>> Rush University Medical Center
>>> Phone: (312) 563-3853
>>> Fax: (312) 563-4660
>>> Email: vy_d...@rush.edu
>>>
>>> 
>>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, October 20, 2011 12:51 PM
>>> To: Vy Dinh
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
>>> autorecon3
>>>
>>> It does need to be there, but usually it creates it's own symbolic link
>>> (so you should not need to copy it).
>>> doug
>>>
>>> Vy Dinh wrote:
>>>
>>>
>>>
>>>> Hi Douglas,
>>>>
>>>> Thank you for your reply. The subdir is just an example, so that is 
>>>> probably a typo in the original post. Fsaverage/ did not exist in 
>>>> SUBJECTS_DIR when we ran the recon commands, so in response to the error, 
>>>> I copied fsaverage/ from the freesurfer directory to my SUBJECTS_DIR. I 
>>>> guess my concern now is whether we need to run the autorecon-all and any 
>>>> subsequent -autorecon processes (with the fsaverage/ folder in 
>>>> SUBJECTS_DIR).
>>>>
>>>> Best,
>>>>
>>>>
>>>> Vy T.U. Dinh
>>>> Research Assistant, Neurological Sciences
>>>> Rush University Medical Center
>>>> Phone: (312) 563-3853
>>>> Fax: (312) 563-4660
>>>> Email: vy_d...@rush.edu
>>>>
>>>> 
>>>> From: Douglas N Greve [gr...@

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

2011-10-21 Thread Douglas N Greve

The BA labels should be in

$FREESURFER_HOME/subjects/fsaverage/label

doug
Vy Dinh wrote:
> 5.0 
>
> Vy T.U. Dinh
> Research Assistant, Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853
> Fax: (312) 563-4660
> Email: vy_d...@rush.edu
>
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Friday, October 21, 2011 9:51 AM
> To: Vy Dinh
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
> autorecon3
>
> So the BA labels don't exist in
> $FREESURFER_HOME/subjects/fsaverage/label? What version are you using?
> doug
>
> Vy Dinh wrote:
>   
>> You're absolutely right. The lh.BA1.label file is missing within 
>> freesurfer/fsaverage. I thought that we may have had the same issue as this 
>> poster 
>> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19399.html) 
>> since we use a mount, but it seems that the missing BA labels is the real 
>> issue. My main concern, then, is how this has affected our processing 
>> (besides not running the BA labels) and whether any reruns would be 
>> necessary. In other words, did recon-all simply skip the BA labels and ran 
>> the other processes or did it crash midway?
>>
>> Also, if you have uploaded a fsaverage folder that contains these missing 
>> files, I will gladly download them from your site. Note that we had run the 
>> recon-all commands with Freesurfer version 5.0. This error was never 
>> encountered until recently (even though we had not upgraded to the newer 
>> version).
>>
>> Thank you for your time,
>>
>>
>> Vy T.U. Dinh
>> Research Assistant, Neurological Sciences
>> Rush University Medical Center
>> Phone: (312) 563-3853
>> Fax: (312) 563-4660
>> Email: vy_d...@rush.edu
>>
>> 
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, October 20, 2011 1:10 PM
>> To: Vy Dinh
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
>> autorecon3
>>
>> No, it means that it cannot find that file.
>> doug
>>
>> Vy Dinh wrote:
>>
>> 
>>> Then does it mean that I can ignore this error message?
>>>
>>> Vy T.U. Dinh
>>> Research Assistant, Neurological Sciences
>>> Rush University Medical Center
>>> Phone: (312) 563-3853
>>> Fax: (312) 563-4660
>>> Email: vy_d...@rush.edu
>>>
>>> 
>>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, October 20, 2011 12:51 PM
>>> To: Vy Dinh
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
>>> autorecon3
>>>
>>> It does need to be there, but usually it creates it's own symbolic link
>>> (so you should not need to copy it).
>>> doug
>>>
>>> Vy Dinh wrote:
>>>
>>>
>>>   
>>>> Hi Douglas,
>>>>
>>>> Thank you for your reply. The subdir is just an example, so that is 
>>>> probably a typo in the original post. Fsaverage/ did not exist in 
>>>> SUBJECTS_DIR when we ran the recon commands, so in response to the error, 
>>>> I copied fsaverage/ from the freesurfer directory to my SUBJECTS_DIR. I 
>>>> guess my concern now is whether we need to run the autorecon-all and any 
>>>> subsequent -autorecon processes (with the fsaverage/ folder in 
>>>> SUBJECTS_DIR).
>>>>
>>>> Best,
>>>>
>>>>
>>>> Vy T.U. Dinh
>>>> Research Assistant, Neurological Sciences
>>>> Rush University Medical Center
>>>> Phone: (312) 563-3853
>>>> Fax: (312) 563-4660
>>>> Email: vy_d...@rush.edu
>>>>
>>>> 
>>>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>>>> Sent: Thursday, October 20, 2011 12:26 PM
>>>> To: Vy Dinh
>>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>>> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
>>>> autorecon3
>>>>
>>>> Does /Users/subdir/ fsaverage exist? Also, it looks like there could be
>>>> a space between "subdir/" and "fsaverage"
>>

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

2011-10-21 Thread Vy Dinh

5.0 

Vy T.U. Dinh
Research Assistant, Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: vy_d...@rush.edu


From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Friday, October 21, 2011 9:51 AM
To: Vy Dinh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
autorecon3

So the BA labels don't exist in
$FREESURFER_HOME/subjects/fsaverage/label? What version are you using?
doug

Vy Dinh wrote:
> You're absolutely right. The lh.BA1.label file is missing within 
> freesurfer/fsaverage. I thought that we may have had the same issue as this 
> poster 
> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19399.html) 
> since we use a mount, but it seems that the missing BA labels is the real 
> issue. My main concern, then, is how this has affected our processing 
> (besides not running the BA labels) and whether any reruns would be 
> necessary. In other words, did recon-all simply skip the BA labels and ran 
> the other processes or did it crash midway?
>
> Also, if you have uploaded a fsaverage folder that contains these missing 
> files, I will gladly download them from your site. Note that we had run the 
> recon-all commands with Freesurfer version 5.0. This error was never 
> encountered until recently (even though we had not upgraded to the newer 
> version).
>
> Thank you for your time,
>
>
> Vy T.U. Dinh
> Research Assistant, Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853
> Fax: (312) 563-4660
> Email: vy_d...@rush.edu
>
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, October 20, 2011 1:10 PM
> To: Vy Dinh
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
> autorecon3
>
> No, it means that it cannot find that file.
> doug
>
> Vy Dinh wrote:
>
>> Then does it mean that I can ignore this error message?
>>
>> Vy T.U. Dinh
>> Research Assistant, Neurological Sciences
>> Rush University Medical Center
>> Phone: (312) 563-3853
>> Fax: (312) 563-4660
>> Email: vy_d...@rush.edu
>>
>> ____________
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, October 20, 2011 12:51 PM
>> To: Vy Dinh
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
>> autorecon3
>>
>> It does need to be there, but usually it creates it's own symbolic link
>> (so you should not need to copy it).
>> doug
>>
>> Vy Dinh wrote:
>>
>>
>>> Hi Douglas,
>>>
>>> Thank you for your reply. The subdir is just an example, so that is 
>>> probably a typo in the original post. Fsaverage/ did not exist in 
>>> SUBJECTS_DIR when we ran the recon commands, so in response to the error, I 
>>> copied fsaverage/ from the freesurfer directory to my SUBJECTS_DIR. I guess 
>>> my concern now is whether we need to run the autorecon-all and any 
>>> subsequent -autorecon processes (with the fsaverage/ folder in 
>>> SUBJECTS_DIR).
>>>
>>> Best,
>>>
>>>
>>> Vy T.U. Dinh
>>> Research Assistant, Neurological Sciences
>>> Rush University Medical Center
>>> Phone: (312) 563-3853
>>> Fax: (312) 563-4660
>>> Email: vy_d...@rush.edu
>>>
>>> 
>>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, October 20, 2011 12:26 PM
>>> To: Vy Dinh
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
>>> autorecon3
>>>
>>> Does /Users/subdir/ fsaverage exist? Also, it looks like there could be
>>> a space between "subdir/" and "fsaverage"
>>> doug
>>>
>>> Vy Dinh wrote:
>>>
>>>
>>>
>>>> Dear Experts,
>>>>
>>>> I ran the wm.mgz corrections and pial corrections using the command:
>>>>
>>>> -autorecon2 –autorecon3 –subjid sub2
>>>>
>>>> However, Freesurfer exited the program with the following message:
>>>>
>>>> SUBJECTS_DIR/Users/subdir
>>>> FREESURFER_HOME Applications/freesurfer
>>>> Loading source label.
>>>> No such file or directory
>>>>

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

2011-10-21 Thread Douglas N Greve

So the BA labels don't exist in 
$FREESURFER_HOME/subjects/fsaverage/label? What version are you using?
doug

Vy Dinh wrote:
> You're absolutely right. The lh.BA1.label file is missing within 
> freesurfer/fsaverage. I thought that we may have had the same issue as this 
> poster 
> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19399.html) 
> since we use a mount, but it seems that the missing BA labels is the real 
> issue. My main concern, then, is how this has affected our processing 
> (besides not running the BA labels) and whether any reruns would be 
> necessary. In other words, did recon-all simply skip the BA labels and ran 
> the other processes or did it crash midway? 
>
> Also, if you have uploaded a fsaverage folder that contains these missing 
> files, I will gladly download them from your site. Note that we had run the 
> recon-all commands with Freesurfer version 5.0. This error was never 
> encountered until recently (even though we had not upgraded to the newer 
> version). 
>
> Thank you for your time,
>
>
> Vy T.U. Dinh
> Research Assistant, Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853
> Fax: (312) 563-4660
> Email: vy_d...@rush.edu
>
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, October 20, 2011 1:10 PM
> To: Vy Dinh
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
> autorecon3
>
> No, it means that it cannot find that file.
> doug
>
> Vy Dinh wrote:
>   
>> Then does it mean that I can ignore this error message?
>>
>> Vy T.U. Dinh
>> Research Assistant, Neurological Sciences
>> Rush University Medical Center
>> Phone: (312) 563-3853
>> Fax: (312) 563-4660
>> Email: vy_d...@rush.edu
>>
>> ________
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, October 20, 2011 12:51 PM
>> To: Vy Dinh
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
>> autorecon3
>>
>> It does need to be there, but usually it creates it's own symbolic link
>> (so you should not need to copy it).
>> doug
>>
>> Vy Dinh wrote:
>>
>> 
>>> Hi Douglas,
>>>
>>> Thank you for your reply. The subdir is just an example, so that is 
>>> probably a typo in the original post. Fsaverage/ did not exist in 
>>> SUBJECTS_DIR when we ran the recon commands, so in response to the error, I 
>>> copied fsaverage/ from the freesurfer directory to my SUBJECTS_DIR. I guess 
>>> my concern now is whether we need to run the autorecon-all and any 
>>> subsequent -autorecon processes (with the fsaverage/ folder in 
>>> SUBJECTS_DIR).
>>>
>>> Best,
>>>
>>>
>>> Vy T.U. Dinh
>>> Research Assistant, Neurological Sciences
>>> Rush University Medical Center
>>> Phone: (312) 563-3853
>>> Fax: (312) 563-4660
>>> Email: vy_d...@rush.edu
>>>
>>> 
>>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>>> Sent: Thursday, October 20, 2011 12:26 PM
>>> To: Vy Dinh
>>> Cc: freesurfer@nmr.mgh.harvard.edu
>>> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
>>> autorecon3
>>>
>>> Does /Users/subdir/ fsaverage exist? Also, it looks like there could be
>>> a space between "subdir/" and "fsaverage"
>>> doug
>>>
>>> Vy Dinh wrote:
>>>
>>>
>>>   
>>>> Dear Experts,
>>>>
>>>> I ran the wm.mgz corrections and pial corrections using the command:
>>>>
>>>> -autorecon2 –autorecon3 –subjid sub2
>>>>
>>>> However, Freesurfer exited the program with the following message:
>>>>
>>>> SUBJECTS_DIR/Users/subdir
>>>> FREESURFER_HOME Applications/freesurfer
>>>> Loading source label.
>>>> No such file or directory
>>>> fsaverage/label/lh.BA1.label
>>>> ERROR reading /Users/subdir/ fsaverage/label/lh.BA1.label
>>>> Darwin mso00820bg.rush.edu <http://mso00820bg.rush.edu> 10.8.0 Darwin
>>>> Kernel Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011;
>>>> root:xnu-1504.15.3~1/RELEASE_I386 i386
>>>>
>>>> recon-all -s sub2 exited with ERRORS at Thu Oct 20 05:12:34

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

2011-10-20 Thread Vy Dinh

You're absolutely right. The lh.BA1.label file is missing within 
freesurfer/fsaverage. I thought that we may have had the same issue as this 
poster 
(http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg19399.html) 
since we use a mount, but it seems that the missing BA labels is the real 
issue. My main concern, then, is how this has affected our processing (besides 
not running the BA labels) and whether any reruns would be necessary. In other 
words, did recon-all simply skip the BA labels and ran the other processes or 
did it crash midway? 

Also, if you have uploaded a fsaverage folder that contains these missing 
files, I will gladly download them from your site. Note that we had run the 
recon-all commands with Freesurfer version 5.0. This error was never 
encountered until recently (even though we had not upgraded to the newer 
version). 

Thank you for your time,


Vy T.U. Dinh
Research Assistant, Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: vy_d...@rush.edu


From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, October 20, 2011 1:10 PM
To: Vy Dinh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
autorecon3

No, it means that it cannot find that file.
doug

Vy Dinh wrote:
> Then does it mean that I can ignore this error message?
>
> Vy T.U. Dinh
> Research Assistant, Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853
> Fax: (312) 563-4660
> Email: vy_d...@rush.edu
>
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, October 20, 2011 12:51 PM
> To: Vy Dinh
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
> autorecon3
>
> It does need to be there, but usually it creates it's own symbolic link
> (so you should not need to copy it).
> doug
>
> Vy Dinh wrote:
>
>> Hi Douglas,
>>
>> Thank you for your reply. The subdir is just an example, so that is probably 
>> a typo in the original post. Fsaverage/ did not exist in SUBJECTS_DIR when 
>> we ran the recon commands, so in response to the error, I copied fsaverage/ 
>> from the freesurfer directory to my SUBJECTS_DIR. I guess my concern now is 
>> whether we need to run the autorecon-all and any subsequent -autorecon 
>> processes (with the fsaverage/ folder in SUBJECTS_DIR).
>>
>> Best,
>>
>>
>> Vy T.U. Dinh
>> Research Assistant, Neurological Sciences
>> Rush University Medical Center
>> Phone: (312) 563-3853
>> Fax: (312) 563-4660
>> Email: vy_d...@rush.edu
>>
>> ________________
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, October 20, 2011 12:26 PM
>> To: Vy Dinh
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
>> autorecon3
>>
>> Does /Users/subdir/ fsaverage exist? Also, it looks like there could be
>> a space between "subdir/" and "fsaverage"
>> doug
>>
>> Vy Dinh wrote:
>>
>>
>>> Dear Experts,
>>>
>>> I ran the wm.mgz corrections and pial corrections using the command:
>>>
>>> -autorecon2 –autorecon3 –subjid sub2
>>>
>>> However, Freesurfer exited the program with the following message:
>>>
>>> SUBJECTS_DIR/Users/subdir
>>> FREESURFER_HOME Applications/freesurfer
>>> Loading source label.
>>> No such file or directory
>>> fsaverage/label/lh.BA1.label
>>> ERROR reading /Users/subdir/ fsaverage/label/lh.BA1.label
>>> Darwin mso00820bg.rush.edu <http://mso00820bg.rush.edu> 10.8.0 Darwin
>>> Kernel Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011;
>>> root:xnu-1504.15.3~1/RELEASE_I386 i386
>>>
>>> recon-all -s sub2 exited with ERRORS at Thu Oct 20 05:12:34 CDT 2011.
>>>
>>> Can someone please explain what this error message means regarding
>>> whether I need to rerun the autorecon processes with the fsaverage
>>> folder within my current subjects folder?  I copied fsaverage/ from
>>> freesurfer/ to my designated SUBJECTS_DIR but have not run the
>>> recon. It seems that the pial surfaces were regenerated while the
>>> white matter segment was not corrected for this one subject. I ran
>>> other subjects within this SUBJECTS_DIR (before I copied the fsaverage
>>> folder) but the white matter segment and pial surfaces were
>>>

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

2011-10-20 Thread Douglas N Greve

No, it means that it cannot find that file.
doug

Vy Dinh wrote:
> Then does it mean that I can ignore this error message?
>
> Vy T.U. Dinh
> Research Assistant, Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853
> Fax: (312) 563-4660
> Email: vy_d...@rush.edu
>
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, October 20, 2011 12:51 PM
> To: Vy Dinh
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
> autorecon3
>
> It does need to be there, but usually it creates it's own symbolic link
> (so you should not need to copy it).
> doug
>
> Vy Dinh wrote:
>   
>> Hi Douglas,
>>
>> Thank you for your reply. The subdir is just an example, so that is probably 
>> a typo in the original post. Fsaverage/ did not exist in SUBJECTS_DIR when 
>> we ran the recon commands, so in response to the error, I copied fsaverage/ 
>> from the freesurfer directory to my SUBJECTS_DIR. I guess my concern now is 
>> whether we need to run the autorecon-all and any subsequent -autorecon 
>> processes (with the fsaverage/ folder in SUBJECTS_DIR).
>>
>> Best,
>>
>>
>> Vy T.U. Dinh
>> Research Assistant, Neurological Sciences
>> Rush University Medical Center
>> Phone: (312) 563-3853
>> Fax: (312) 563-4660
>> Email: vy_d...@rush.edu
>>
>> ____________
>> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
>> Sent: Thursday, October 20, 2011 12:26 PM
>> To: Vy Dinh
>> Cc: freesurfer@nmr.mgh.harvard.edu
>> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
>> autorecon3
>>
>> Does /Users/subdir/ fsaverage exist? Also, it looks like there could be
>> a space between "subdir/" and "fsaverage"
>> doug
>>
>> Vy Dinh wrote:
>>
>> 
>>> Dear Experts,
>>>
>>> I ran the wm.mgz corrections and pial corrections using the command:
>>>
>>> -autorecon2 –autorecon3 –subjid sub2
>>>
>>> However, Freesurfer exited the program with the following message:
>>>
>>> SUBJECTS_DIR/Users/subdir
>>> FREESURFER_HOME Applications/freesurfer
>>> Loading source label.
>>> No such file or directory
>>> fsaverage/label/lh.BA1.label
>>> ERROR reading /Users/subdir/ fsaverage/label/lh.BA1.label
>>> Darwin mso00820bg.rush.edu <http://mso00820bg.rush.edu> 10.8.0 Darwin
>>> Kernel Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011;
>>> root:xnu-1504.15.3~1/RELEASE_I386 i386
>>>
>>> recon-all -s sub2 exited with ERRORS at Thu Oct 20 05:12:34 CDT 2011.
>>>
>>> Can someone please explain what this error message means regarding
>>> whether I need to rerun the autorecon processes with the fsaverage
>>> folder within my current subjects folder?  I copied fsaverage/ from
>>> freesurfer/ to my designated SUBJECTS_DIR but have not run the
>>> recon. It seems that the pial surfaces were regenerated while the
>>> white matter segment was not corrected for this one subject. I ran
>>> other subjects within this SUBJECTS_DIR (before I copied the fsaverage
>>> folder) but the white matter segment and pial surfaces were
>>> regenerated for them. Looking forward to your responses.
>>>
>>> Thank you,
>>>
>>> Vy T.U. Dinh
>>> Research Assistant, Neurological Sciences
>>> Rush University Medical Center
>>> Phone: (312) 563-3853
>>> Fax: (312) 563-4660
>>> Email: vy_d...@rush.edu <mailto:vy_d...@rush.edu>
>>> 
>>>
>>> ___
>>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>>
>>
>>
>> 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

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

2011-10-20 Thread Vy Dinh

Then does it mean that I can ignore this error message?

Vy T.U. Dinh
Research Assistant, Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: vy_d...@rush.edu


From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, October 20, 2011 12:51 PM
To: Vy Dinh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
autorecon3

It does need to be there, but usually it creates it's own symbolic link
(so you should not need to copy it).
doug

Vy Dinh wrote:
> Hi Douglas,
>
> Thank you for your reply. The subdir is just an example, so that is probably 
> a typo in the original post. Fsaverage/ did not exist in SUBJECTS_DIR when we 
> ran the recon commands, so in response to the error, I copied fsaverage/ from 
> the freesurfer directory to my SUBJECTS_DIR. I guess my concern now is 
> whether we need to run the autorecon-all and any subsequent -autorecon 
> processes (with the fsaverage/ folder in SUBJECTS_DIR).
>
> Best,
>
>
> Vy T.U. Dinh
> Research Assistant, Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853
> Fax: (312) 563-4660
> Email: vy_d...@rush.edu
>
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, October 20, 2011 12:26 PM
> To: Vy Dinh
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
> autorecon3
>
> Does /Users/subdir/ fsaverage exist? Also, it looks like there could be
> a space between "subdir/" and "fsaverage"
> doug
>
> Vy Dinh wrote:
>
>> Dear Experts,
>>
>> I ran the wm.mgz corrections and pial corrections using the command:
>>
>> -autorecon2 –autorecon3 –subjid sub2
>>
>> However, Freesurfer exited the program with the following message:
>>
>> SUBJECTS_DIR/Users/subdir
>> FREESURFER_HOME Applications/freesurfer
>> Loading source label.
>> No such file or directory
>> fsaverage/label/lh.BA1.label
>> ERROR reading /Users/subdir/ fsaverage/label/lh.BA1.label
>> Darwin mso00820bg.rush.edu <http://mso00820bg.rush.edu> 10.8.0 Darwin
>> Kernel Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011;
>> root:xnu-1504.15.3~1/RELEASE_I386 i386
>>
>> recon-all -s sub2 exited with ERRORS at Thu Oct 20 05:12:34 CDT 2011.
>>
>> Can someone please explain what this error message means regarding
>> whether I need to rerun the autorecon processes with the fsaverage
>> folder within my current subjects folder?  I copied fsaverage/ from
>> freesurfer/ to my designated SUBJECTS_DIR but have not run the
>> recon. It seems that the pial surfaces were regenerated while the
>> white matter segment was not corrected for this one subject. I ran
>> other subjects within this SUBJECTS_DIR (before I copied the fsaverage
>> folder) but the white matter segment and pial surfaces were
>> regenerated for them. Looking forward to your responses.
>>
>> Thank you,
>>
>> Vy T.U. Dinh
>> Research Assistant, Neurological Sciences
>> Rush University Medical Center
>> Phone: (312) 563-3853
>> Fax: (312) 563-4660
>> Email: vy_d...@rush.edu <mailto:vy_d...@rush.edu>
>> 
>>
>> ___
>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
>
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html


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

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

2011-10-20 Thread Douglas N Greve

It does need to be there, but usually it creates it's own symbolic link 
(so you should not need to copy it).
doug

Vy Dinh wrote:
> Hi Douglas,
>
> Thank you for your reply. The subdir is just an example, so that is probably 
> a typo in the original post. Fsaverage/ did not exist in SUBJECTS_DIR when we 
> ran the recon commands, so in response to the error, I copied fsaverage/ from 
> the freesurfer directory to my SUBJECTS_DIR. I guess my concern now is 
> whether we need to run the autorecon-all and any subsequent -autorecon 
> processes (with the fsaverage/ folder in SUBJECTS_DIR).
>
> Best,
>
>
> Vy T.U. Dinh
> Research Assistant, Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853
> Fax: (312) 563-4660
> Email: vy_d...@rush.edu
>
> 
> From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
> Sent: Thursday, October 20, 2011 12:26 PM
> To: Vy Dinh
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
> autorecon3
>
> Does /Users/subdir/ fsaverage exist? Also, it looks like there could be
> a space between "subdir/" and "fsaverage"
> doug
>
> Vy Dinh wrote:
>   
>> Dear Experts,
>>
>> I ran the wm.mgz corrections and pial corrections using the command:
>>
>> -autorecon2 –autorecon3 –subjid sub2
>>
>> However, Freesurfer exited the program with the following message:
>>
>> SUBJECTS_DIR/Users/subdir
>> FREESURFER_HOME Applications/freesurfer
>> Loading source label.
>> No such file or directory
>> fsaverage/label/lh.BA1.label
>> ERROR reading /Users/subdir/ fsaverage/label/lh.BA1.label
>> Darwin mso00820bg.rush.edu <http://mso00820bg.rush.edu> 10.8.0 Darwin
>> Kernel Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011;
>> root:xnu-1504.15.3~1/RELEASE_I386 i386
>>
>> recon-all -s sub2 exited with ERRORS at Thu Oct 20 05:12:34 CDT 2011.
>>
>> Can someone please explain what this error message means regarding
>> whether I need to rerun the autorecon processes with the fsaverage
>> folder within my current subjects folder?  I copied fsaverage/ from
>> freesurfer/ to my designated SUBJECTS_DIR but have not run the
>> recon. It seems that the pial surfaces were regenerated while the
>> white matter segment was not corrected for this one subject. I ran
>> other subjects within this SUBJECTS_DIR (before I copied the fsaverage
>> folder) but the white matter segment and pial surfaces were
>> regenerated for them. Looking forward to your responses.
>>
>> Thank you,
>>
>> Vy T.U. Dinh
>> Research Assistant, Neurological Sciences
>> Rush University Medical Center
>> Phone: (312) 563-3853
>> Fax: (312) 563-4660
>> Email: vy_d...@rush.edu <mailto:vy_d...@rush.edu>
>> 
>>
>> ___
>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
>
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
Freesurfer mailing list
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Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

2011-10-20 Thread Vy Dinh

Hi Douglas,

Thank you for your reply. The subdir is just an example, so that is probably a 
typo in the original post. Fsaverage/ did not exist in SUBJECTS_DIR when we ran 
the recon commands, so in response to the error, I copied fsaverage/ from the 
freesurfer directory to my SUBJECTS_DIR. I guess my concern now is whether we 
need to run the autorecon-all and any subsequent -autorecon processes (with the 
fsaverage/ folder in SUBJECTS_DIR).

Best,

Vy T.U. Dinh
Research Assistant, Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: vy_d...@rush.edu

From: Douglas N Greve [gr...@nmr.mgh.harvard.edu]
Sent: Thursday, October 20, 2011 12:26 PM
To: Vy Dinh
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & 
autorecon3

Does /Users/subdir/ fsaverage exist? Also, it looks like there could be
a space between "subdir/" and "fsaverage"
doug

Vy Dinh wrote:
> Dear Experts,
>
> I ran the wm.mgz corrections and pial corrections using the command:
>
> -autorecon2 –autorecon3 –subjid sub2
>
> However, Freesurfer exited the program with the following message:
>
> SUBJECTS_DIR/Users/subdir
> FREESURFER_HOME Applications/freesurfer
> Loading source label.
> No such file or directory
> fsaverage/label/lh.BA1.label
> ERROR reading /Users/subdir/ fsaverage/label/lh.BA1.label
> Darwin mso00820bg.rush.edu <http://mso00820bg.rush.edu> 10.8.0 Darwin
> Kernel Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011;
> root:xnu-1504.15.3~1/RELEASE_I386 i386
>
> recon-all -s sub2 exited with ERRORS at Thu Oct 20 05:12:34 CDT 2011.
>
> Can someone please explain what this error message means regarding
> whether I need to rerun the autorecon processes with the fsaverage
> folder within my current subjects folder?  I copied fsaverage/ from
> freesurfer/ to my designated SUBJECTS_DIR but have not run the
> recon. It seems that the pial surfaces were regenerated while the
> white matter segment was not corrected for this one subject. I ran
> other subjects within this SUBJECTS_DIR (before I copied the fsaverage
> folder) but the white matter segment and pial surfaces were
> regenerated for them. Looking forward to your responses.
>
> Thank you,
>
> Vy T.U. Dinh
> Research Assistant, Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853
> Fax: (312) 563-4660
> Email: vy_d...@rush.edu <mailto:vy_d...@rush.edu>
> 
>
> ___
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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] Freesurfer Error Message in running autorecon2 & autorecon3

2011-10-20 Thread Douglas N Greve

Does /Users/subdir/ fsaverage exist? Also, it looks like there could be 
a space between "subdir/" and "fsaverage"
doug

Vy Dinh wrote:
> Dear Experts,
>
> I ran the wm.mgz corrections and pial corrections using the command:
>
> -autorecon2 –autorecon3 –subjid sub2
>
> However, Freesurfer exited the program with the following message:
>
> SUBJECTS_DIR/Users/subdir
> FREESURFER_HOME Applications/freesurfer
> Loading source label.
> No such file or directory
> fsaverage/label/lh.BA1.label
> ERROR reading /Users/subdir/ fsaverage/label/lh.BA1.label
> Darwin mso00820bg.rush.edu  10.8.0 Darwin 
> Kernel Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011; 
> root:xnu-1504.15.3~1/RELEASE_I386 i386
>
> recon-all -s sub2 exited with ERRORS at Thu Oct 20 05:12:34 CDT 2011. 
>
> Can someone please explain what this error message means regarding 
> whether I need to rerun the autorecon processes with the fsaverage 
> folder within my current subjects folder?  I copied fsaverage/ from 
> freesurfer/ to my designated SUBJECTS_DIR but have not run the 
> recon. It seems that the pial surfaces were regenerated while the 
> white matter segment was not corrected for this one subject. I ran 
> other subjects within this SUBJECTS_DIR (before I copied the fsaverage 
> folder) but the white matter segment and pial surfaces were 
> regenerated for them. Looking forward to your responses. 
>
> Thank you,
>
> Vy T.U. Dinh
> Research Assistant, Neurological Sciences
> Rush University Medical Center
> Phone: (312) 563-3853
> Fax: (312) 563-4660
> Email: vy_d...@rush.edu 
> 
>
> ___
> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

___
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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] Freesurfer Error Message in running autorecon2 & autorecon3

2011-10-20 Thread Vy Dinh

Dear Experts,

I ran the wm.mgz corrections and pial corrections using the command:

-autorecon2 –autorecon3 –subjid sub2

However, Freesurfer exited the program with the following message:

SUBJECTS_DIR/Users/subdir
FREESURFER_HOME Applications/freesurfer
Loading source label.
No such file or directory
fsaverage/label/lh.BA1.label
ERROR reading /Users/subdir/ fsaverage/label/lh.BA1.label
Darwin mso00820bg.rush.edu 10.8.0 Darwin Kernel 
Version 10.8.0: Tue Jun  7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 
i386

recon-all -s sub2 exited with ERRORS at Thu Oct 20 05:12:34 CDT 2011.

Can someone please explain what this error message means regarding whether I 
need to rerun the autorecon processes with the fsaverage folder within my 
current subjects folder?  I copied fsaverage/ from freesurfer/ to my designated 
SUBJECTS_DIR but have not run the recon. It seems that the pial surfaces were 
regenerated while the white matter segment was not corrected for this one 
subject. I ran other subjects within this SUBJECTS_DIR (before I copied the 
fsaverage folder) but the white matter segment and pial surfaces were 
regenerated for them. Looking forward to your responses.

Thank you,

Vy T.U. Dinh
Research Assistant, Neurological Sciences
Rush University Medical Center
Phone: (312) 563-3853
Fax: (312) 563-4660
Email: vy_d...@rush.edu
___
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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.

Re: [Freesurfer] Freesurfer-Error message

Re: [Freesurfer] Freesurfer-Error message

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[Freesurfer] Freesurfer-Error message

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

Re: [Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

[Freesurfer] Freesurfer Error Message in running autorecon2 & autorecon3

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