fixes behav in singl-session-subjects in long study

[fliem]

This is the revived PR #22.
In longitudinal studies (studies in which at least one subject has more than one session) and --multiple_sessions='longitudinal') subjects with only one session should undergo the entire longitudinal stream. The changes in #11 broke that behavior. The present changes should fix it.

• The longitudinal check was moved to the top, as it needs to loop through all subjects and look for sessions, before running the recon-all commands in a second loop.
• At the moment longitudinal test cases cannot be run as they take >2h (longitudinal tests #23).
• I've made the test1 check for a recon-all.done file after it is done.

[alexlicohen]

The run.py code change looks like it would reset longitudinal_study which each subject it checks, thus would be set by how many sessions the last subject has, vs the if any of the subjects had multiple sessions.

[fliem]

Thanks. I reverted to my very first implementation that searches for the first multi-sessions subject and stops if it is found. I've also added a multi_session_study variable to make things clearer.

[alexlicohen]

That looks right... you could also just set longitudinal_study to False above the loop, then break when set to True on line 100, without an additional variable and drop the else conditional on line 105

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---------------------------------------------------------------- Alexander Li Cohen, M.D., Ph.D. E-mail: Alexander.Cohen2@childrens.harvard.edu (Medical/Science Email) E-mail: alexcohen@gmail.com (Lifetime Email) ----------------------------------------------------------------

On Tue, Jan 31, 2017 at 12:40 PM, Franz Liem ***@***.***> wrote: Thanks. I reverted to my very first implementation that searches for the first multi-sessions subject and stops if it is found. I've also added a multi_session_study variable to make things clearer. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#24 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AIPa_7-LfNS4OaaZAoDQJCwwoiU5ow3Bks5rX3IAgaJpZM4LyWXr> .

[fliem]

My thinking was that it might not hurt to have this variable for later.

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Am 31.01.2017 um 18:45 schrieb Alexander Li Cohen ***@***.***>: That looks right... you could also just set longitudinal_study to False above the loop, then break when set to True on line 100, without an additional variable and drop the else conditional on line 105 ---------------------------------------------------------------- Alexander Li Cohen, M.D., Ph.D. E-mail: ***@***.*** (Medical/Science Email) E-mail: ***@***.*** (Lifetime Email) ---------------------------------------------------------------- On Tue, Jan 31, 2017 at 12:40 PM, Franz Liem ***@***.***> wrote: > Thanks. I reverted to my very first implementation that searches for the > first multi-sessions subject and stops if it is found. I've also added a > multi_session_study variable to make things clearer. > > — > You are receiving this because you commented. > Reply to this email directly, view it on GitHub > <#24 (comment)>, > or mute the thread > <https://github.com/notifications/unsubscribe-auth/AIPa_7-LfNS4OaaZAoDQJCwwoiU5ow3Bks5rX3IAgaJpZM4LyWXr> > . > — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#24 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFgWC6w2BD0HHby1guQBrXdZwQAyy4Ofks5rX3McgaJpZM4LyWXr>.