Hi Lea,

sorry for the late reply, just in case this is still of interest:

1. It is possible to process all cross data with 5.3 and then base and 
long with 6.0. As long as you do the same for all subjects it should be 
fine, just don't mix across subjects. Also depending on the size if only 
half the cross are already processed it may make sense to re-do 
everything with 6.0 to have a clean and easy setup.

2. Basically yes, but there are some situations where things can go 
wrong, for example

  - you restart long_submit_jobs, but not all scheduled jobs are running 
(e.g. some are still in the queue), it would then resubmit those jobs

- Jobs die and the is_running file still exists in the freesurfer 
scripts dir, in that case long_submit_jobs will not re-submit those jobs

Best, Martin

Am 27.02.2018 um 11:23 schrieb Backhausen, Lea:
> Hi Martin,
> thank you so much for your detailed answer. I will see how we can implement 
> these modifications.
> Just two quick follow up questions:
> 1) I have half of the data already processed with the CROSS step using FS 
> 5.3.0. Is it possible to use this data when running the TEMPLATE and LONG 
> steps with FS 6.0.0 or would this corrupt results?
> 2) Our HPC system is known to have problems from time to time and jobs end up 
> being killed. If the long_submit_jobs job gets killed prematurely would it 
> just resume processing the data that hasn't been processed yet if I submit 
> this job/script again?
> Thanks again for your help!
> Best,
> Lea Backhausen
> Research assistant
> Klinik und Poliklinik für Kinder- und Jugendpsychiatrie und –psychotherapie
> Universitätsklinikum Carl Gustav Carus
> an der Technischen Universität Dresden
> Anstalt des öffentlichen Rechts des Freistaates Sachsen
> Fetscherstraße 74, 01307 Dresden
> http://www.uniklinikum-dresden.de
> -----Original Message-----
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of 
> freesurfer-requ...@nmr.mgh.harvard.edu
> Sent: Thursday, February 22, 2018 5:33 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Freesurfer Digest, Vol 168, Issue 34
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> Message: 1
> Date: Wed, 21 Feb 2018 18:26:32 -0500
> From: Douglas N Greve <gr...@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Search angle limitation in the flirt
>       registration
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID: <1e86b3d8-54c6-c9ad-54b3-7cc8df81c...@nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset=utf-8; format=flowed
> you should post your question to the FSL list (they developed and support 
> flirt)
> On 02/21/2018 05:34 PM, Yixin Ma wrote:
>> Hi freesurfer developers and users,
>> I'm writing to ask about the search angle limitation (--searchrx, --
>> searchry and --searchrz) in the flirt function. I use the search angle
>> option a lot for limited angle search, which usually generate a better
>> registration result compared with the broad angle search. But I still
>> don't quite understand how rx,ry and rz are defined and how negative
>> and positive angles affect the result. Because sometimes I find the
>> result after the angle limitation does not align well with my
>> expectation of rotation angle.
>> Thank you for your help,
>> Yixin Ma
>> Brain Image and Analysis Center
>> Duke university
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>> Freesurfer@nmr.mgh.harvard.edu
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