Re: [Freesurfer] Cannot open FreeSurfer application zipped file

2016-01-26 Thread Meirelles, Osorio (NIH/NIA/IRP) [E] 
Hi Lee,

   I ran the command " sha1sum 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz" and I got the result  
7c03e796e9b81ee69aaa60079c4094f20b945c08 where it should have been 
0c8d784e28a435bd5ea45be6a461990894cfc5b7  , according to the webpage:
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/sha1sum.txt

   So does this mean that I have a Freesurfer  corrupted installation file?  
What would you recommend?  Can you suggest me a link to download a  more 
updated version? 

  Thanks,

  Osorio

-Original Message-
From: Meirelles, Osorio (NIH/NIA/IRP) [E] 
Sent: Monday, December 28, 2015 2:07 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cannot open FreeSurfer application zipped file

Hi Lee,

 I guess it worked.   It looks like several hundreds  of files were unzipped., 
however, in the end, there was still the following message:

gzip: stdin: unexpected end of file
tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now

At this stage I do not know if this is a minor error or if there were many more 
files to be unzipped that were not since the process was interrupted.

 What would you recommend I do next?

Thank you,

Osorio

-Original Message-
From: Lee Tirrell [mailto:ltirr...@nmr.mgh.harvard.edu] 
Sent: Monday, December 28, 2015 1:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cannot open FreeSurfer application zipped file

Hi Osorio,

Are you sure the file completely downloaded without errors? You can confirm 
this by running:

sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

The output of this command should match the result on this webpage:
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/sha1sum.txt

If your file is uncorrupted, try running this command to unzip it:

tar xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

Best,
Lee

On Mon, 28 Dec 2015, Meirelles, Osorio (NIH/NIA/IRP) [E] wrote:

> Dear experts,
>
>   I tried to unzip the file  
> “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
>
>I entered on my command prompt: “gunzip 
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the 
> message after a few minutes:“gzip: 
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of 
> file”
>
>Perhaps this might be a version issue.  Anyway, any help into getting the 
> correct installation file would be greatly appreciated.
>
>   Thanks,
>
>   Osorio
>
> -Original Message-
> From: Meirelles, Osorio (NIH/NIA/IRP) [E]
> Sent: Thursday, December 24, 2015 12:23 PM
> To: Freesurfer support list
> Cc: Matthew Glasser
> Subject: RE: [Freesurfer] hello freesurfer developer~
>
> Dear experts,
>
>   I tried to unzip the file  
> “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
>
>I entered on my command prompt: “gunzip 
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the 
> message after a few minutes:“gzip: 
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of 
> file”
>
>Perhaps this might be a version issue.  Anyway, any help into getting the 
> correct installation file would be greatly appreciated.
>
>   Thanks,
>
>   Osorio
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, December 24, 2015 12:16 PM
> To: Freesurfer support list
> Cc: Matthew Glasser
> Subject: Re: [Freesurfer] hello freesurfer developer~
>
> Hi A-reum
>
> you should probably ask the Wash U HCP group. I'll cc Matt Glasser who
> might be able to answer your question
> cheers
> Bruce
>
> On Thu, 24 Dec 2015, A-reum Min wrote:
>
>> hello experts!my name is areum.
>> i have some question to you.
>> a few days ago i was down load HCP(human connectom project) data.
>> but.. how can i use these HCP format.
>> i have never seen before these format(fig.1.png)
>> I want to see HCP data subjects's cortical thickness using qdec.
>> how can i to do? 
>> plz answer me  
>>
>> 2015-11-10 7:49 GMT+09:00 A-reum Min :
>>   Hello experts!
>> I have some question to you..
>>
>> I don't need to show up so small blue regions(fig.1 blue region)
>>
>> How can i control these? 
>>
>> 2015-11-10 7:41 GMT+09:00 Douglas N Greve :
>>   Hi, please create a new thread since this is a new topic.
>>   Also, I don't
>>   understand your question so please elaborate.
>>
>>   On 11/09/2015 05:34 AM, A-reum Min wrote:
>>  > Hello experts!
>>  >
>>  > i have some question to

Re: [Freesurfer] Cannot open FreeSurfer application zipped file

2015-12-28 Thread Meirelles, Osorio (NIH/NIA/IRP) [E] 
Hi Lee,

 I guess it worked.   It looks like several hundreds  of files were unzipped., 
however, in the end, there was still the following message:

gzip: stdin: unexpected end of file
tar: Unexpected EOF in archive
tar: Unexpected EOF in archive
tar: Error is not recoverable: exiting now

At this stage I do not know if this is a minor error or if there were many more 
files to be unzipped that were not since the process was interrupted.

 What would you recommend I do next?

Thank you,

Osorio

-Original Message-
From: Lee Tirrell [mailto:ltirr...@nmr.mgh.harvard.edu] 
Sent: Monday, December 28, 2015 1:46 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cannot open FreeSurfer application zipped file

Hi Osorio,

Are you sure the file completely downloaded without errors? You can confirm 
this by running:

sha1sum freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

The output of this command should match the result on this webpage:
http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/sha1sum.txt

If your file is uncorrupted, try running this command to unzip it:

tar xzvf freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz

Best,
Lee

On Mon, 28 Dec 2015, Meirelles, Osorio (NIH/NIA/IRP) [E] wrote:

> Dear experts,
>
>   I tried to unzip the file  
> “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
>
>I entered on my command prompt: “gunzip 
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the 
> message after a few minutes:“gzip: 
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of 
> file”
>
>Perhaps this might be a version issue.  Anyway, any help into getting the 
> correct installation file would be greatly appreciated.
>
>   Thanks,
>
>   Osorio
>
> -Original Message-
> From: Meirelles, Osorio (NIH/NIA/IRP) [E]
> Sent: Thursday, December 24, 2015 12:23 PM
> To: Freesurfer support list
> Cc: Matthew Glasser
> Subject: RE: [Freesurfer] hello freesurfer developer~
>
> Dear experts,
>
>   I tried to unzip the file  
> “freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder.
>
>I entered on my command prompt: “gunzip 
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the 
> message after a few minutes:“gzip: 
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of 
> file”
>
>Perhaps this might be a version issue.  Anyway, any help into getting the 
> correct installation file would be greatly appreciated.
>
>   Thanks,
>
>   Osorio
>
> -Original Message-
> From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, December 24, 2015 12:16 PM
> To: Freesurfer support list
> Cc: Matthew Glasser
> Subject: Re: [Freesurfer] hello freesurfer developer~
>
> Hi A-reum
>
> you should probably ask the Wash U HCP group. I'll cc Matt Glasser who
> might be able to answer your question
> cheers
> Bruce
>
> On Thu, 24 Dec 2015, A-reum Min wrote:
>
>> hello experts!my name is areum.
>> i have some question to you.
>> a few days ago i was down load HCP(human connectom project) data.
>> but.. how can i use these HCP format.
>> i have never seen before these format(fig.1.png)
>> I want to see HCP data subjects's cortical thickness using qdec.
>> how can i to do? 
>> plz answer me  
>>
>> 2015-11-10 7:49 GMT+09:00 A-reum Min :
>>   Hello experts!
>> I have some question to you..
>>
>> I don't need to show up so small blue regions(fig.1 blue region)
>>
>> How can i control these? 
>>
>> 2015-11-10 7:41 GMT+09:00 Douglas N Greve :
>>   Hi, please create a new thread since this is a new topic.
>>   Also, I don't
>>   understand your question so please elaborate.
>>
>>   On 11/09/2015 05:34 AM, A-reum Min wrote:
>>  > Hello experts!
>>  >
>>  > i have some question to you..
>>  >
>>  > How can i control the cluster size?
>>  >
>>  > My cluster threshold is 1.
>>  >
>>  > then, too many blue regions (as shown fig.1).
>>  >
>>  > so, i want to control cluster threshold 1--> cluster
>>   threshold 5.
>>  >
>>  > 2015-11-08 20:44 GMT+09:00 A-reum Min
>>   >  > <mailto:naniy...@gmail.com>>:
>>  >
>>  >     Hello bruce!
>>  >
>>  >     I solve the problem for your answer.
>>  >
>>  >     And.. i have some question to you..
>>  >
>>  >     How

[Freesurfer] Cannot open FreeSurfer application zipped file

2015-12-28 Thread Meirelles, Osorio (NIH/NIA/IRP) [E] 
Dear experts,

   I tried to unzip the file  
“freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder. 

I entered on my command prompt: “gunzip 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the 
message after a few minutes:“gzip: 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of 
file”
   
Perhaps this might be a version issue.  Anyway, any help into getting the 
correct installation file would be greatly appreciated.

   Thanks,

   Osorio

-Original Message-
From: Meirelles, Osorio (NIH/NIA/IRP) [E] 
Sent: Thursday, December 24, 2015 12:23 PM
To: Freesurfer support list
Cc: Matthew Glasser
Subject: RE: [Freesurfer] hello freesurfer developer~

Dear experts,

   I tried to unzip the file  
“freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” in my UNIX folder. 

I entered on my command prompt: “gunzip 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz” and then got the 
message after a few minutes:“gzip: 
freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz: unexpected end of 
file”
   
Perhaps this might be a version issue.  Anyway, any help into getting the 
correct installation file would be greatly appreciated.

   Thanks,

   Osorio

-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] 
Sent: Thursday, December 24, 2015 12:16 PM
To: Freesurfer support list
Cc: Matthew Glasser
Subject: Re: [Freesurfer] hello freesurfer developer~

Hi A-reum

you should probably ask the Wash U HCP group. I'll cc Matt Glasser who 
might be able to answer your question
cheers
Bruce

On Thu, 24 Dec 2015, A-reum Min wrote:

> hello experts!my name is areum.
> i have some question to you.
> a few days ago i was down load HCP(human connectom project) data.
> but.. how can i use these HCP format.
> i have never seen before these format(fig.1.png)
> I want to see HCP data subjects's cortical thickness using qdec.
> how can i to do? 
> plz answer me  
> 
> 2015-11-10 7:49 GMT+09:00 A-reum Min :
>   Hello experts!
> I have some question to you..
> 
> I don't need to show up so small blue regions(fig.1 blue region)
> 
> How can i control these? 
> 
> 2015-11-10 7:41 GMT+09:00 Douglas N Greve :
>   Hi, please create a new thread since this is a new topic.
>   Also, I don't
>   understand your question so please elaborate.
>
>   On 11/09/2015 05:34 AM, A-reum Min wrote:
>   > Hello experts!
>   >
>   > i have some question to you..
>   >
>   > How can i control the cluster size?
>   >
>   > My cluster threshold is 1.
>   >
>   > then, too many blue regions (as shown fig.1).
>   >
>   > so, i want to control cluster threshold 1--> cluster
>   threshold 5.
>   >
>   > 2015-11-08 20:44 GMT+09:00 A-reum Min
>  > >:
>   >
>   >     Hello bruce!
>   >
>   >     I solve the problem for your answer.
>   >
>   >     And.. i have some question to you..
>   >
>   >     How can i control the cluster size?
>   >
>   >     My cluster threshold is 1.
>   >
>   >     then, too many blue regions (as shown fig.1).
>   >
>   >     so, i want to control cluster threshold 1--> cluster
>   threshold 5.
>   >
>   >     How can i to do?
>   >
>   >
>   >
>   >
>   >
>   >     2015-11-05 22:22 GMT+09:00 Bruce Fischl
>   >        >:
>   >
>   >         are
>   /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm
>   >         and
>   /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm
>   >         images from *different* series or from the
>   *same* series? If
>   >         they are in the same series than that explains
>   what is
>   >         happening. You should only give recon-all a
>   single file from
>   >         any one acquisition - it will figure out the
>   rest of the files
>   >         that are part of it.
>   >
>   >         cheers
>   >         Bruce
>   >
>   >
>   >         On Thu, 5 Nov 2015, A-reum Min wrote:
>   >
>   >             hello experts.
>   >             i have some question to  you...
>   >
>   >             when i enter the recon-all -i /paht~
>   >
>   >             error showed up like below one..
>   >
>   >             how can i to fix it?
>   >
>   >             [areum@localhost 0165766_1]# recon-all -i
>   >           
>    /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm
>   -i
>   >           
>    /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm
>   >             -all -s sub002
>   >             Subject Stamp:
>   >           
>    freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>   >             Current Stamp:
>   >