Dear Anastasia and Christopher, I could run the new version and greaty appreciate your advices. Thank you for everything!
Anri ********************************************************************** 京都府立医科大学附属病院 精神科・心療内科 渡辺 杏里 ********************************************************************** Anri WATANABE, M.D. Department of Psychiatry, University Hospital, Kyoto Prefectural University of Medicine ********************************************************************** 2014-12-16 3:31 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu>: > > > Yes, download the update, unzip it, and copy the new files over the old > files in the $FREESURFER_HOME/bin directory. Until you do that you'll be > using the old version. > > > On Mon, 15 Dec 2014, Anri WATANABE wrote: > > Yes, I guess I'm running the old version. >> Is this right that I should overwrite some old scripts in "bin" file? >> >> Many thanks, >> Anri >> >> >> >> ********************************************************************** >> 京都府立医科大学附属病院 >> 精神科・心療内科 >> 渡辺 杏里 >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto Prefectural University of Medicine >> ********************************************************************** >> >> 2014-12-13 7:27 GMT+09:00 Chris Watson <Christopher.Watson@childrens. >> harvard.edu>: >> No, she is saying that you should open a terminal, and type only >> "trac-all". This should display >> the help for that program, including the program's flags. If you >> don't see "-qa" listed, then the >> trac-all you're using is an older version. >> You need to verify that you have downloaded the latest version and >> overwritten the older one (or >> change your $PATH to look for the newer one). >> >> >> On 12/11/2014 09:38 PM, Anri WATANABE wrote: >> Thanks, Anastasia. I'm worried about that a quality assessment step >> is not run because >> there are no presentation about "-qa" when I type "trac-all" in >> terminal (other steps are >> presented.) >> Do you mean QA step will be run even if no mention about it? >> >> Thanks in advance, >> Anri >> >> >> >> ********************************************************************** >> 京都府立医科大学附属病院 >> 精神科・心療内科 >> 渡辺 杏里 >> ********************************************************************** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto Prefectural University of Medicine >> ********************************************************************** >> >> 2014-12-12 4:48 GMT+09:00 Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu >> >: >> >> Hi Anri - This is not a command itself, it's an option of the >> trac-all command. So >> you need to run: >> trac-all -qa -c the_name_of_your_configuration_file >> >> Or, if you just run the entire preprocessing: >> trac-all -prep -c the_name_of_your_configuration_file >> then the motion QA measures will be computed by default as one of >> the many steps of >> the preprocessing. >> >> You can run "trac-all" without any arguments to see usage >> information on all the the >> different options. >> >> Hope this helps, >> a.y >> >> On Tue, 9 Dec 2014, Anri WATANABE wrote: >> >> Thank you, Anastasia. >> I had downloaded the updated software and unzipped it, but I >> couldn't >> find >> the command "-qa." >> I found "-qa" in the trac-all text file in the updated >> software. >> However there are no "-qa" in terminal when I run "trac-all." >> Do I have to move the file somewhere? >> >> ************************************************************ >> ********** >> 京都府立医科大学附属病院 >> 精神科・心療内科 >> 渡辺 杏里 >> ************************************************************ >> ********** >> Anri WATANABE, M.D. >> Department of Psychiatry, >> University Hospital, Kyoto Prefectural University of Medicine >> ************************************************************ >> ********** >> >> 2014-11-22 7:22 GMT+09:00 Anastasia Yendiki >> <ayend...@nmr.mgh.harvard.edu>: >> >> Hi Anri - See here, and follow the link "software >> update": >> >> http://surfer.nmr.mgh.harvard. >> edu/fswiki/trac-all#Arguments >> >> The -qa option was added after 5.3 was released. >> >> a.y >> >> On Mon, 10 Nov 2014, Anri WATANABE wrote: >> >> Dear FreeSurfer experts, >> >> I'm running pre-processing steps in TRACULA >> separatelly and could neither find the context >> about >> quality >> assessment step nor run the command 'trac-all -qa >> -c >> <configulation file>. >> I downloaded TRACULA in FreeSurfer 5.3, MacOSX >> lion >> (64-bit). >> Could anyone solve this problem? >> Thank you. >> >> Anri >> >> >> >> ************************************************************ >> ********** >> 京都府立医科大学附属病院 >> 精神科・心療内科 >> 渡辺 杏里 >> >> ************************************************************ >> ********** >> WATANABE ANRI >> Department of Psychiatry, >> University Hospital, Kyoto Prefectural University >> of >> Medicine >> >> ************************************************************ >> ********** >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the >> person to whom >> it is >> addressed. 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If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > >
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