Re: [Freesurfer] Recon-all -long

[Martin Reuter]

Hi Jürgen,

mainly you are right. As there is no change in the first processing
steps between the cross sectional and the longitudinal stream, it is
sufficient, to simply copy that data from the cross sectional
directories, instead of rerunning it.
The -long stream starts being different in the skullstrip step (where
additionally information from the base template is used). 

For a detailed description of each step see:

http://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing 


Cheers, Martin

On Tue, 2009-11-24 at 15:42 +0100, Jürgen Hänggi wrote:
> Dear FS experts
> 
> Am I right that the input for step 3 in recon-all -long are the already
> cross-sectionally processed images from step 1 and not the raw images that I
> used to create these cross-sectionally images?
> 
> Thanks for clarification
> Regards
> Jürgen
> 
> 
> Jürgen Hänggi, Ph.D.
> Division Neuropsychology
> Institute of Psychology
> University of Zurich
> Binzmuehlestrasse 14, PO Box 25
> 8050 Zurich, Switzerland
> 0041 44 635 73 97 (phone office)
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> j.haenggi[at]psychologie.uzh.ch (email)
> http://www.psychologie.uzh.ch/neuropsy/ (website)
> http://www.juergenhaenggi.ch (private website)
> 
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Re: [Freesurfer] script to check multiple cases with tksurfer

[Martin Reuter]

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
> 
> 
> 
> 
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Re: [Freesurfer] script to check multiple cases with tksurfer

[Bruce Fischl]

you can also write a tcl script to save snapshots to a file and invoke it 
with -tcl 

[Freesurfer] Destrieux Atlas (aparc.a2009s.annot)

[Dalwani, Manish]

Hi Freesurfers,

Where can I find documentation and labels for Destrieux Atlas? How can I 
download 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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