On 03/03/2016 02:46 PM, Ji Won Bang wrote: > Thanks for your reply. It works. > > I have 1 more general question. > > When running: mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_day1 > > I get 2 files (template.log & template.nii.gz) under the functional > subdirectory(bold_day1) and under each run(001, 002 etc). > > When I run: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_day1 -per-run > > Does that command use the template for motion correction that was > created under each run? Not the one under the functional subdirectory? It uses the one under each run. > > My understanding of mktemplate-sess and mc-sess is that > mktemplate-sess produces the template per each run (saves the template > file under each run) and/or the template per session(?) (saves the > template file under the functional subdirectory). > > Then mc-sess utilizes the template for motion correction. > If I use -per-run, mc-sess utilizes the template file created per each > run and if I use -per-session, mc-see utilizes the template file > created per session(file under the functional subdirectory). > > Is my understanding correct? Yes > > Thanks a lot! > > Best, > Ji Won > > 2016-03-03 12:36 GMT-05:00 Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>>: > > you have to use -per-run not -per-session > > > On 03/03/2016 12:27 PM, Ji Won Bang wrote: > > The command I used is: > > > > mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_retino > > > > mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -per-session > > > > Thank you. > > > > Best, > > Ji Won > > > > > > > > 2016-03-03 12:22 GMT-05:00 Ji Won Bang <kirsten...@gmail.com > <mailto:kirsten...@gmail.com> > > <mailto:kirsten...@gmail.com <mailto:kirsten...@gmail.com>>>: > > > > Dear. freesurfer experts. > > > > Hi. I'm using freesurfer version 5.3.0. > > > > I tried mc-sess onto runs that have different number of slices. > > > > However, due to this different number of slices in different > runs, > > mc-sess gives an error. > > > > I expected that running mc-sess in freesurfer version 5.3.0 > would > > handle this issue. > > > > If you can share your idea to fix this problem, that would be a > > great help. > > > > Thank you! > > > > Best, > > Ji Won > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
