From mpsampat@gmail.com Tue Nov 24 20:19:32 2009
From: Mehul Sampat <mpsampat@gmail.com>
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] script to check multiple cases with tksurfer
Date: Tue, 24 Nov 2009 17:19:26 -0800
Message-ID: <fd015cf80911241719x5b38a331y32e00795aa7ff972@mail.gmail.com>
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Hi Folks,

I would like to visually check the cortical parcellation for a large number
of  patients  (>200) using tksurfer.
Is there a script to which I could submit a list of subject id's and get it
to
launch tksurfer and display the parcellation data for each subject
sequentially ?

Thanks
Mehul



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From mreuter@nmr.mgh.harvard.edu Wed Nov 25 10:08:24 2009
From: Martin Reuter <mreuter@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] script to check multiple cases with tksurfer
Date: Wed, 25 Nov 2009 10:08:18 -0500
Message-ID: <1259161698.5202.362.camel@riemann.nmr.mgh.harvard.edu>
In-Reply-To: <fd015cf80911241719x5b38a331y32e00795aa7ff972@mail.gmail.com>
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How about:

setenv SUBJECTS " id1 id2 id3 .. "

foreach s ($SUBJECTS)
 # do stuff
 echo $s
 tksurfer $s ....
end

(this is for cshell) 

Cheers, Martin

On Tue, 2009-11-24 at 17:19 -0800, Mehul Sampat wrote:
> Hi Folks,
> 
> I would like to visually check the cortical parcellation for a large
> number of  patients  (>200) using tksurfer. 
> Is there a script to which I could submit a list of subject id's and
> get it to 
> launch tksurfer and display the parcellation data for each subject
> sequentially ? 
> 
> Thanks
> Mehul
> 
> 
> 
> 
> _______________________________________________
> Freesurfer mailing list
> Freesurfer(a)nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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From fischl@nmr.mgh.harvard.edu Wed Nov 25 10:23:52 2009
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] script to check multiple cases with tksurfer
Date: Wed, 25 Nov 2009 10:23:48 -0500
Message-ID: <Pine.LNX.4.62.0911251022310.4502@gate.nmr.mgh.harvard.edu>
In-Reply-To: <1259161698.5202.362.camel@riemann.nmr.mgh.harvard.edu>
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you can also write a tcl script to save snapshots to a file and invoke it 
with -tcl <script name>

the script would look something like

set fname snapshot.$subject.tif
save_tiff $fname
exit


cheers,
Bruce

On Wed, 25 Nov 2009, Martin Reuter wrote:

> How about:
>
> setenv SUBJECTS " id1 id2 id3 .. "
>
> foreach s ($SUBJECTS)
> # do stuff
> echo $s
> tksurfer $s ....
> end
>
> (this is for cshell)
>
> Cheers, Martin
>
> On Tue, 2009-11-24 at 17:19 -0800, Mehul Sampat wrote:
>> Hi Folks,
>>
>> I would like to visually check the cortical parcellation for a large
>> number of  patients  (>200) using tksurfer.
>> Is there a script to which I could submit a list of subject id's and
>> get it to
>> launch tksurfer and display the parcellation data for each subject
>> sequentially ?
>>
>> Thanks
>> Mehul
>>
>>
>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer(a)nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer(a)nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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From Manish.Dalwani@ucdenver.edu Wed Nov 25 15:06:52 2009
From: "Dalwani, Manish" <Manish.Dalwani@ucdenver.edu>
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Destrieux Atlas (aparc.a2009s.annot)
Date: Wed, 25 Nov 2009 13:06:45 -0700
Message-ID: <30167E70C34FA042954B76E3BEF818EC985908136C@CORTEZ.ucdenver.pvt>
In-Reply-To: <Pine.LNX.4.62.0911251022310.4502@gate.nmr.mgh.harvard.edu>
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Hi Freesurfers,

Where can I find documentation and labels for Destrieux Atlas? How can I down=
load this new atlas? My stats folders for each subject has aparc.a2005s.stats=
. Can I generate the stats for the new atlas?

Sincerely,
Manish Dalwani
Sr. PRA
Univ. of CO


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